1 Background

This report shows the analysis performed for metagenomics sequencing from the gut microbiome of 66 pregnant women. For each pregnant woman, samples were taken at 1 to 3 different time points during the pregnancy (i.e. corresponding to trimesters, up until day ~280 when the child is born) to give a total of 134 samples. From the 66 pregnant women, XXX are diabetic (T1D). For some analyses, time points were categorised into trimesters, correspondence being:

Trimester 1 = 0-99 days Trimester 2 = 100-196 days Trimester 3 = 196-280 days

2 Background

This report shows the analysis performed for metagenomics sequencing from the gut microbiome of 70 pregnancies (36 in women with T1D) from a total of 66 different women. For each pregnant woman, samples were taken at 1 to 3 different time points during the pregnancy (i.e. corresponding to trimesters, up until day ~280 when the child is born) to give a total of 134 samples. From the 32 pregnant women, 16 are diabetic (T1D). For some analyses, time points were categorised into trimesters, correspondence being:

Trimester 1 = 0-99 days Trimester 2 = 100-196 days Trimester 3 = 196-280 days

3 Data generation

Samples were shotgun sequenced using the NovaSeq 6000 illumina sequencing machine at the Ramaciotti Centre for Genomics located at the University of New South Wales (UNSW) in Sydney, Australia.

3.1 Processing the sequences: from sequence data to feature table

The data was processed through pipelines developed by the group of Curtis Huttenhower at Harvard Univerisity and Broad Institute. These pipelines belong to the BioBakery.

The raw data was uploaded to the short read archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra/) with accession number PRJNA604850.

KneadData (https://bitbucket.org/biobakery/biobakery/wiki/kneaddata) was used to filter human (“contaminant”) sequences as well as quality controlling the sequences This has to be done for each sample. Example:

kneaddata –input 4_S1_R1_001.fastq.gz –input 4_S1_R2_001.fastq.gz -db /home/users/allstaff/schulze.a/bin/Kneaddata/Homo_sapiens –trimmomatic /usr/local/bioinfsoftware/trimmomatic/trimmomatic-0.36 –output ./kneaddata_output -t 12

HUMAnN2 (https://bitbucket.org/biobakery/humann2/wiki/Home) was employed to quantify gene families and pathways; and within HUMANn2, Metaphlan was also used to obtain taxonomic profiles. This process is also performed per sample and read pair1 and read pair2 need to be concatenated and saved in the same file prior to running HUMAn2 (i.e. end-pairing relationships are currently not taken into account during HUMAnN2’s alignment steps. This is due to the fact that HUMAnN2 strictly aligns reads to isolated coding sequences: either at the nucleotide level or through translated search. As such, it will frequently be the case that one read (READ1) will map inside a given coding sequence while its mate-pair (READ2) will not [information obtained from the manual]). Example of running HUMAnN2 with a sample:

humann2 -i NGU5366A1.fastq -o ./Output_HUMAnN2 –threads 28

Running this outputs several files, among those is “NGU5366A1_metaphlan_bugs_list.tsv”, which is a list of the bacterial taxa found in that sample at all taxonomic levels (i.e. stratified data) and their relative normalizaed abundances. The script merge_metaphlan_tables.py was used to merge the MetaPhlAn output from several samples into one table taxa (rows) vs samples (columns) with the table enlisting the relative normalized abundances per sample per taxa. Example:

merge_metaphlan_tables.py metaphlan_output1.txt metaphlan_output2.txt metaphlan_output3.txt > ./merged_abundance_table_Rel_Abundance.txt

As mentioned above, the abundance table (profile) contains the stratified data. In order to obtain a table that contains the taxa at a specific taxonomic level (e.g. Species), grep was used. Example for species taxonomic level:

grep ’s__’ merged_abundance_table_Rel_Abundance.txt | grep -v ’t’ > merged_abundance_table_Rel_Abundance_Sp.tsv # -v (exclude) ’t’ will prevent from selecting those lines that have species and strain (’t__’) classification. We just need species in this case.

Example for genus taxonomic level:

grep ’g__’ merged_abundance_table_Rel_Abundance.txt | grep -v ’t’ | grep -v ’s’ > merged_abundance_table_Rel_Abundance_Genus.tsv

Note: For other taxonomic levels, this process was repeated for each taxonomic level.

This table contains the whole taxonomy for each taxa, from “kindom” to “Species” along with per sample abundances (i.e. counts per million [CPM]). From this table the taxonomy was obtained. The taxa table is then transformed into a biom file in JSON format and the taxonomic and metadata infomation were added with the software biom. Example:

biom convert -i merged_abundance_table_Rel_Abundance_Sp.tsv -o merged_abundance_table_Rel_Abundance_Sp.biom –table-type=“OTU table” –to-json
biom add-metadata –sc-separated taxonomy –observation-header OTUID,taxonomy –observation-metadata-fp Species_taxonomy.txt -i merged_abundance_table_Rel_Abundance_Sp.biom -o Pregnancy_NovaSeq_taxonomic_profile_Rel_Species_NV_wTax.biom
biom add-metadata -i Pregnancy_NovaSeq_taxonomic_profile_Rel_Species_NV_wTax.biom -o Pregnancy_NovaSeq_taxonomic_profile_Rel_Species_NV_wTaxMet.biom –sample-metadata-fp ./metadata.csv

This process was repeated at for each taxonomic level.

The resulting taxa tables (one for each taxonomic level) with taxonomies and metadata were imported into R to process with the Phyloseq (https://github.com/joey711/phyloseq) and other packages. The data were first de-identified (i.e. data relating to the identification of the donor was removed) and R objects were saved (i.e. A total of 6 taxonomic and 3 functional files were generated). Those R objects were used as inputs in the analysis performed in this document. These objects and other files used in this markdown can be found at https://github.com/PapenfussLab/RothSchulze_pregnancy-gut-microbiome-T1D and all the paths needs to be changed in this document in order to reproduce the analysis.

4 Bar plots taxonomy

5 Alpha diversity

5.1 Alpha diversity (T1D vs. non-T1D continuous time [Days])


Call:
geeglm(formula = Observed ~ t1dfactor * days_c + age_c + nullip + 
    bmi_c + HLA, data = DivCal_R_df, id = motherid, corstr = "exchangeable")

 Coefficients:
                    Estimate  Std.err     Wald Pr(>|W|)    
(Intercept)         96.81936  2.39884 1629.005   <2e-16 ***
t1dfactorT1D         2.08666  2.12628    0.963   0.3264    
days_c              -0.01196  0.01817    0.433   0.5106    
age_c               -0.66073  0.27302    5.857   0.0155 *  
nullipYes           -4.17930  2.37889    3.086   0.0789 .  
bmi_c               -0.14664  0.20923    0.491   0.4834    
HLADRXX             -3.12808  2.91574    1.151   0.2833    
HLAGroup3o4         -4.01888  2.66817    2.269   0.1320    
t1dfactorT1D:days_c -0.02969  0.02971    0.998   0.3177    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Correlation structure = exchangeable 
Estimated Scale Parameters:

            Estimate Std.err
(Intercept)    134.1   20.13
  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha   0.2475  0.1093
Number of clusters:   121  Maximum cluster size: 3 

5.2 Alpha diversity (time continuous [see T1D vs. non-T1D])


Call:
geeglm(formula = Observed ~ t1dfactor * Tri + age_c + nullip + 
    bmi_c + HLA, data = DivCal_R_df, id = motherid, corstr = "exchangeable")

 Coefficients:
                   Estimate Std.err   Wald Pr(>|W|)    
(Intercept)          98.423   3.460 809.34   <2e-16 ***
t1dfactorT1D          4.508   4.165   1.17    0.279    
TriT2                -1.151   3.170   0.13    0.717    
TriT3                -1.690   3.183   0.28    0.596    
age_c                -0.676   0.270   6.25    0.012 *  
nullipYes            -4.315   2.350   3.37    0.066 .  
bmi_c                -0.180   0.213   0.71    0.399    
HLADRXX              -3.501   3.012   1.35    0.245    
HLAGroup3o4          -4.497   2.766   2.64    0.104    
t1dfactorT1D:TriT2   -0.614   5.047   0.01    0.903    
t1dfactorT1D:TriT3   -4.127   5.140   0.64    0.422    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Correlation structure = exchangeable 
Estimated Scale Parameters:

            Estimate Std.err
(Intercept)      135      20
  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha    0.258   0.127
Number of clusters:   121  Maximum cluster size: 3 

6 Species taxonomic level

6.1 Microbial community composition analysis at Species level (Beta diversity analysi)

Hypothesis

Hypothesis: the gut microbiome taxonomic composition (i.e. Beta diversity) during pregnancy differs between women with and without T1D. In order to test if this hypothesis holds true, a measurement of the distance between each pair of samples is calculated (i.e. Bray-Curtis) and a repeated measure aware permutational analysis of variance (i.e. RMA-PERMANOVA) test is applied. A P-value <0.05 is considered to be significant, meaning that our hypothesis cannot be rejected. Borderline P-values are also considered positive.

Problems with the available R function for Beta diversity analysis

The current available function for performing hypothesis testing of differences in the microbiome composition between groups of samples is called Adonis (i.e. which perform a PERMANOVA test) and is part of the Rpackage vegan (Oksanen, J. et al). The main problem with this function is that if the metadata of interest does not vary with time (e.g. disease status, sex, etc.), adonis does not calculate the corresponding P value correctly, as it permutes levels within a subject. This does not make sense for something like disease status or sex as permuting within-subject will produce the exact same distribution each time you permute. This a known drawback of the adonis function for repeated measures.

In order to get the correct P-value for a time-invariant metadata, the permutation procedure has to be altered such that it permutes the subjects rather than levels within subjects, which apply to our current pregnancy dataset.

Here I'm running a script written by Jason Lloyd-Price from Curtis Huttenhower lab in Harvard. This script is being used instead of the regular Adonis (PERMANOVA test) from the R package Vegan because as stated above, our metadata of interest (i.e. T1D status) does not vary with time, we have a mixture of data which changes within and between an individual and we also have unequal group sizes (i.e. we do not always have exactly 3 samples per woman). For those three reasons, it was recommended to use his script to perform the RMA-PERMANOVA analysis.

PARAMETERS:

permute_within: This data frame has samples on rows and metadata on columns. This should only contain metadata that varies within a block (i.e. it's a single-column data frame with only time/Days).Since, the other metadata within the block should be the same between repeated measurements and this will not hold when we introduce other factor i.e. sequencing run, BMI, parity, gestational age (i.e. Days or trimester) and conception age , those five factors should be placed here

blocks: This should just be a vector giving the group of each sample (i.e. the motherid vector; motherid is strictly accounting for personID but not for pregnancy per se).

block_data: This data frame contains per-block metadata, with one row per block (motherid). It should only contain metadata pertaining to the blocks (i.e. T1Dstatus). motherid is not numeric, ensure that the row names match the factor names in the motherid vector (blocks).

metadata_order: This is needed if you want to specify a particular order that the model should be fit in. Metadata earlier in the list will be fit and residualized first, so these should be features we are NOT interested in and want to control for.

Results from PERMANOVA test with repeat measure-aware permutations - Controlling for Days/Trimester, sequencing run, conception age, BMI, parity and HLA type

Here the blocking factor is taking into account each mother who might have given samples from different trimesters or two different pregnancies (i.e. motherid is the name of the factor). Therefore, the factor "motherid" takes into account two different pregnancies from the same mother as one SubjectID to adjust for repeated measurements

The interaction between T1D status and time was also included in order to test if the differences between T1D and non-T1D women in the same or changes throguhout pregnancy.

6.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
seqRun                 4      1.49   0.372    1.84 0.050  0.492   
Days                   1      0.27   0.270    1.33 0.009  0.217   
T1D_Time_Interaction   1      0.70   0.702    3.47 0.023  0.004 **
Age                    1      0.53   0.535    2.64 0.018  0.493   
Parity                 1      0.54   0.535    2.64 0.018  0.616   
BMI                    1      0.53   0.527    2.60 0.018  0.998   
HLA                    2      1.13   0.563    2.78 0.038  0.080 . 
T1Dstatus              1      0.30   0.300    1.48 0.010  0.885   
Residuals            121     24.49   0.202         0.817  0.186   
Total                133     29.97                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.004

Due to the interaction between T1D and time having a significant P-value, differences in beta diversity between T1D and non-T1D was assessed by trimester using a normal PERMANOVA with the adonis function.

6.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3      0.55   0.184   0.792 0.110   0.88
Nulliparous     1      0.33   0.329   1.417 0.066   0.10
Age_LMP         1      0.23   0.234   1.009 0.047   0.45
BMI_conception  1      0.25   0.255   1.098 0.051   0.35
HLA.6DRML       2      0.34   0.172   0.743 0.069   0.89
T1Dstatus       1      0.27   0.274   1.181 0.055   0.28
Residuals      13      3.02   0.232         0.603       
Total          22      5.01                 1.000       
[1] 0.283

Beta diversity Plot

6.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3      1.07   0.356    1.89 0.117  0.001 ***
Age        1      0.29   0.290    1.55 0.032  0.172    
Parity     1      0.34   0.340    1.81 0.037  0.001 ***
BMI        1      0.21   0.213    1.13 0.023  0.680    
HLA        2      0.68   0.339    1.80 0.074  0.074 .  
T1Dstatus  1      0.36   0.361    1.92 0.039  0.105    
Residuals 33      6.20   0.188         0.678  0.031 *  
Total     42      9.15                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

6.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
seqRun     4      0.86   0.214   0.962 0.056  0.566   
Age        1      0.24   0.240   1.078 0.016  0.386   
Parity     1      0.27   0.270   1.214 0.018  0.617   
BMI        1      0.39   0.385   1.734 0.025  0.874   
HLA        2      0.49   0.245   1.101 0.032  0.388   
T1Dstatus  1      0.45   0.451   2.030 0.029  0.003 **
Residuals 57     12.67   0.222         0.825  0.107   
Total     67     15.36                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

6.1.5 Trimester 3 sensitivity analysis

For Species P-T1Dstatus= 0.008
For Strain P-T1Dstatus= 0.003
For Genus P-T1Dstatus= 0.042
For Family P-T1Dstatus= 0.041
For Order P-T1Dstatus= 0.1
For Phylum P-T1Dstatus= 0.094

6.1.6 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.95   0.477    2.62 0.065  0.285  
seqRun     3      1.31   0.436    2.40 0.089  0.702  
Age        1      0.43   0.430    2.36 0.029  0.950  
Parity     1      0.55   0.552    3.03 0.038  0.067 .
BMI        1      0.66   0.662    3.64 0.045  0.515  
Days       1      0.22   0.219    1.20 0.015  0.097 .
Residuals 58     10.55   0.182         0.719  0.252  
Total     67     14.68                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

6.1.7 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.95   0.477    2.61 0.065  0.312  
seqRun     3      1.31   0.436    2.39 0.089  0.699  
Age        1      0.43   0.430    2.36 0.029  0.944  
Parity     1      0.55   0.552    3.03 0.038  0.043 *
BMI        1      0.66   0.662    3.63 0.045  0.526  
Tri        2      0.37   0.187    1.02 0.025  0.041 *
Residuals 57     10.40   0.182         0.708  0.181  
Total     67     14.68                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

6.1.8 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.25   0.625    3.27 0.086  0.054 .
seqRun     4      1.31   0.329    1.72 0.090  0.987  
Age        1      0.65   0.652    3.41 0.045  0.015 *
Parity     1      0.47   0.470    2.46 0.032  0.737  
BMI        1      0.18   0.183    0.96 0.013  1.000  
Days       1      0.22   0.220    1.15 0.015  0.287  
Residuals 55     10.51   0.191         0.720  0.147  
Total     65     14.60                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

6.1.9 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.25   0.625    3.24 0.086  0.054 .
seqRun     4      1.31   0.329    1.70 0.090  0.975  
Age        1      0.65   0.652    3.38 0.045  0.012 *
Parity     1      0.47   0.470    2.43 0.032  0.720  
BMI        1      0.18   0.183    0.95 0.013  0.999  
Tri        2      0.30   0.150    0.78 0.021  0.713  
Residuals 54     10.43   0.193         0.714  0.272  
Total     65     14.60                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

6.1.10 Other factors

6.1.10.1 Age at conception

6.1.10.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.17   0.585    2.87 0.039  0.087 .
T1Dstatus              1      0.77   0.769    3.78 0.026  0.014 *
seqRun                 4      1.50   0.374    1.84 0.050  0.500  
Tri                    2      0.39   0.193    0.95 0.013  0.628  
Age                    1      0.55   0.549    2.70 0.018  0.301  
Parity                 1      0.47   0.467    2.29 0.016  0.901  
BMI                    1      0.54   0.540    2.65 0.018  0.846  
Age_Time_Interaction   1      0.16   0.161    0.79 0.005  0.278  
Residuals            120     24.43   0.204         0.815  0.025 *
Total                133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.17   0.585    2.87 0.039  0.095 .
T1Dstatus              1      0.77   0.769    3.77 0.026  0.017 *
seqRun                 4      1.50   0.374    1.83 0.050  0.515  
Tri                    2      0.39   0.193    0.95 0.013  0.596  
Age                    1      0.55   0.549    2.69 0.018  0.289  
Parity                 1      0.47   0.467    2.29 0.016  0.905  
BMI                    1      0.54   0.540    2.64 0.018  0.851  
Age_Time_Interaction   1      0.10   0.098    0.48 0.003  0.470  
Residuals            120     24.49   0.204         0.817  0.032 *
Total                133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.17   0.585    2.87 0.039  0.086 .
T1Dstatus              1      0.77   0.769    3.77 0.026  0.022 *
seqRun                 4      1.50   0.374    1.84 0.050  0.512  
Tri                    2      0.39   0.193    0.95 0.013  0.602  
Age                    1      0.55   0.549    2.69 0.018  0.286  
Parity                 1      0.47   0.467    2.29 0.016  0.919  
BMI                    1      0.54   0.540    2.65 0.018  0.842  
Age_Time_Interaction   1      0.12   0.125    0.61 0.004  0.544  
Residuals            120     24.47   0.204         0.816  0.038 *
Total                133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.1.4 Age at conception (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      1.17   0.585    2.88 0.039  0.091 .
T1Dstatus   1      0.77   0.769    3.78 0.026  0.020 *
seqRun      4      1.50   0.374    1.84 0.050  0.524  
Tri         2      0.39   0.193    0.95 0.013  0.621  
Parity      1      0.47   0.468    2.30 0.016  0.933  
BMI         1      0.53   0.533    2.62 0.018  0.833  
Age         1      0.56   0.555    2.73 0.019  0.288  
Residuals 121     24.59   0.203         0.821  0.023 *
Total     133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.1.5 Age at conception (no interaction: trimester 1)

Call:
adonis(formula = D ~ SeqRun + Nulliparous + BMI_conception +      HLA.6DRML + T1Dstatus + Age_LMP, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3      0.55   0.184   0.792 0.110   0.88
Nulliparous     1      0.33   0.329   1.417 0.066   0.10
BMI_conception  1      0.26   0.263   1.133 0.053   0.29
HLA.6DRML       2      0.38   0.190   0.817 0.076   0.79
T1Dstatus       1      0.29   0.288   1.241 0.058   0.20
Age_LMP         1      0.18   0.178   0.765 0.035   0.77
Residuals      13      3.02   0.232         0.603       
Total          22      5.01                 1.000       
6.1.10.1.6 Age at conception (no interaction: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.73   0.366    1.95 0.080  0.083 .
T1Dstatus  1      0.43   0.435    2.31 0.048  0.046 *
seqRun     3      0.98   0.325    1.73 0.107  0.700  
Parity     1      0.29   0.293    1.56 0.032  0.891  
BMI        1      0.22   0.217    1.16 0.024  0.501  
Age        1      0.30   0.296    1.58 0.032  0.278  
Residuals 33      6.20   0.188         0.678  0.038 *
Total     42      9.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.10.2 Age at conception (no interaction: trimester 3)


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.56   0.282   1.270 0.037  0.189   
T1Dstatus  1      0.44   0.435   1.958 0.028  0.006 **
seqRun     4      0.85   0.213   0.957 0.055  0.819   
Parity     1      0.27   0.271   1.220 0.018  0.513   
BMI        1      0.33   0.331   1.490 0.022  0.959   
Age        1      0.24   0.238   1.069 0.015  0.317   
Residuals 57     12.67   0.222         0.825  0.107   
Total     67     15.36                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.10.3 Body max index (BMI)

6.1.10.3.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.17   0.585    2.87 0.039  0.114  
T1Dstatus              1      0.77   0.769    3.77 0.026  0.021 *
seqRun                 4      1.50   0.374    1.84 0.050  0.520  
Tri                    2      0.39   0.193    0.95 0.013  0.659  
Age                    1      0.55   0.549    2.69 0.018  0.289  
Parity                 1      0.47   0.467    2.29 0.016  0.905  
BMI                    1      0.54   0.540    2.65 0.018  0.834  
BMI_Time_Interaction   1      0.12   0.119    0.59 0.004  0.597  
Residuals            120     24.47   0.204         0.817  0.046 *
Total                133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.3.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.17   0.585    2.87 0.039  0.096 .
T1Dstatus              1      0.77   0.769    3.77 0.026  0.018 *
seqRun                 4      1.50   0.374    1.83 0.050  0.500  
Tri                    2      0.39   0.193    0.95 0.013  0.612  
Age                    1      0.55   0.549    2.69 0.018  0.293  
Parity                 1      0.47   0.467    2.29 0.016  0.914  
BMI                    1      0.54   0.540    2.65 0.018  0.832  
BMI_Time_Interaction   1      0.10   0.102    0.50 0.003  0.895  
Residuals            120     24.49   0.204         0.817  0.042 *
Total                133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.3.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.17   0.585    2.88 0.039  0.093 .
T1Dstatus              1      0.77   0.769    3.78 0.026  0.017 *
seqRun                 4      1.50   0.374    1.84 0.050  0.527  
Tri                    2      0.39   0.193    0.95 0.013  0.636  
Age                    1      0.55   0.549    2.70 0.018  0.280  
Parity                 1      0.47   0.467    2.30 0.016  0.922  
BMI                    1      0.54   0.540    2.66 0.018  0.845  
BMI_Time_Interaction   1      0.20   0.197    0.97 0.007  0.290  
Residuals            120     24.39   0.203         0.814  0.025 *
Total                133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.3.4 BMI (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      1.17   0.585    2.88 0.039  0.093 .
T1Dstatus   1      0.77   0.769    3.78 0.026  0.025 *
seqRun      4      1.50   0.374    1.84 0.050  0.517  
Tri         2      0.39   0.193    0.95 0.013  0.634  
Age         1      0.55   0.549    2.70 0.018  0.309  
Parity      1      0.47   0.467    2.30 0.016  0.901  
BMI         1      0.54   0.540    2.66 0.018  0.850  
Residuals 121     24.59   0.203         0.821  0.043 *
Total     133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.10.4 HLA type

6.1.10.4.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.17   0.585    2.89 0.039  0.084 .
T1Dstatus              1      0.77   0.769    3.79 0.026  0.018 *
Days                   1      0.28   0.280    1.38 0.009  0.282  
seqRun                 4      1.47   0.367    1.81 0.049  0.495  
Age                    1      0.54   0.543    2.68 0.018  0.352  
Parity                 1      0.48   0.478    2.36 0.016  0.875  
BMI                    1      0.53   0.531    2.62 0.018  0.860  
HLA_Time_Interaction   1      0.19   0.193    0.95 0.006  1.000  
Residuals            121     24.54   0.203         0.819  0.231  
Total                133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.4.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.17   0.585    2.88 0.039  0.105  
T1Dstatus              1      0.77   0.769    3.78 0.026  0.017 *
Days                   1      0.28   0.280    1.38 0.009  0.344  
seqRun                 4      1.47   0.367    1.80 0.049  0.510  
Age                    1      0.54   0.543    2.67 0.018  0.350  
Parity                 1      0.48   0.478    2.35 0.016  0.872  
BMI                    1      0.53   0.531    2.61 0.018  0.832  
HLA_Time_Interaction   1      0.12   0.122    0.60 0.004  1.000  
Residuals            121     24.61   0.203         0.821  0.314  
Total                133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.4.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      1.17   0.585    2.88 0.039  0.094 .
T1Dstatus              1      0.77   0.769    3.78 0.026  0.022 *
Days                   1      0.28   0.280    1.38 0.009  0.299  
seqRun                 4      1.47   0.367    1.80 0.049  0.490  
Age                    1      0.54   0.543    2.67 0.018  0.339  
Parity                 1      0.48   0.478    2.35 0.016  0.884  
BMI                    1      0.53   0.531    2.61 0.018  0.840  
HLA_Time_Interaction   1      0.15   0.154    0.76 0.005  0.998  
Residuals            121     24.58   0.203         0.820  0.066 .
Total                133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.4.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days        1      0.32   0.318    1.57 0.011  0.130  
seqRun      4      1.44   0.360    1.77 0.048  0.743  
Age         1      0.54   0.538    2.66 0.018  0.469  
Parity      1      0.54   0.537    2.65 0.018  0.375  
BMI         1      0.58   0.579    2.86 0.019  0.955  
T1Dstatus   1      0.67   0.673    3.32 0.022  0.045 *
HLA         2      1.15   0.576    2.84 0.038  0.067 .
Residuals 122     24.73   0.203         0.825  0.020 *
Total     133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.4.5 HLA (no interaction: T1)

Call:
adonis(formula = D ~ SeqRun + Nulliparous + BMI_conception +      T1Dstatus + Age_LMP + HLA.6DRML, data = Meta_df) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3      0.55   0.184   0.792 0.110  0.886  
Nulliparous     1      0.33   0.329   1.417 0.066  0.097 .
BMI_conception  1      0.26   0.263   1.133 0.053  0.296  
T1Dstatus       1      0.32   0.322   1.389 0.064  0.099 .
Age_LMP         1      0.19   0.188   0.810 0.038  0.717  
HLA.6DRML       2      0.33   0.167   0.721 0.067  0.923  
Residuals      13      3.02   0.232         0.603         
Total          22      5.01                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.4.6 HLA type (no interaction: T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
Days       1      0.30   0.296    1.56 0.032   0.56
seqRun     3      1.05   0.351    1.85 0.115   0.46
Age        1      0.29   0.289    1.53 0.032   0.51
Parity     1      0.33   0.333    1.76 0.036   0.81
BMI        1      0.22   0.220    1.16 0.024   0.88
T1Dstatus  1      0.32   0.324    1.71 0.035   0.17
HLA        2      0.58   0.289    1.52 0.063   0.23
Residuals 32      6.06   0.189         0.662   0.17
Total     42      9.15                 1.000       
6.1.10.4.7 HLA type (no interaction: T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
Days       1      0.30   0.302   1.349 0.020   0.70
seqRun     4      0.83   0.208   0.931 0.054   0.58
Age        1      0.24   0.236   1.054 0.015   0.44
Parity     1      0.27   0.274   1.223 0.018   0.52
BMI        1      0.38   0.375   1.678 0.024   0.95
T1Dstatus  1      0.30   0.300   1.341 0.020   0.16
HLA        2      0.51   0.256   1.143 0.033   0.29
Residuals 56     12.53   0.224         0.816   0.40
Total     67     15.36                 1.000       

6.1.10.5 Parity

6.1.10.5.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                         Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                       2      1.17   0.585    2.89 0.039  0.102  
T1Dstatus                 1      0.77   0.769    3.79 0.026  0.012 *
Days                      1      0.28   0.280    1.38 0.009  0.311  
seqRun                    4      1.47   0.367    1.81 0.049  0.485  
Age                       1      0.54   0.543    2.68 0.018  0.343  
Parity                    1      0.48   0.478    2.36 0.016  0.866  
BMI                       1      0.53   0.531    2.62 0.018  0.836  
Parity_Time_Interaction   1      0.19   0.193    0.95 0.006  0.151  
Residuals               121     24.54   0.203         0.819  0.020 *
Total                   133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.5.2 Parity (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      1.17   0.585    2.89 0.039  0.083 .
T1Dstatus   1      0.77   0.769    3.79 0.026  0.014 *
Days        1      0.28   0.280    1.38 0.009  0.318  
seqRun      4      1.47   0.367    1.81 0.049  0.492  
BMI         1      0.60   0.597    2.95 0.020  0.896  
Age         1      0.55   0.547    2.70 0.018  0.394  
Parity      1      0.41   0.407    2.01 0.014  0.801  
Residuals 122     24.73   0.203         0.825  0.016 *
Total     133     29.97                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.10.6 Mode of delivery

6.1.10.6.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.17   0.585    2.95 0.039  0.101   
T1Dstatus              1      0.77   0.769    3.87 0.026  0.020 * 
MOD                    2      0.99   0.496    2.50 0.033  0.317   
Days                   1      0.29   0.288    1.45 0.010  0.226   
seqRun                 4      1.36   0.339    1.71 0.045  0.857   
Age                    1      0.66   0.663    3.34 0.022  0.006 **
Parity                 1      0.41   0.411    2.07 0.014  0.971   
BMI                    1      0.51   0.514    2.59 0.017  0.810   
MOD_Time_Interaction   1      0.19   0.193    0.97 0.006  1.000   
Residuals            119     23.61   0.198         0.788  0.206   
Total                133     29.97                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.6.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.17   0.585    2.94 0.039  0.096 . 
T1Dstatus              1      0.77   0.769    3.86 0.026  0.022 * 
MOD                    2      0.99   0.496    2.50 0.033  0.304   
Days                   1      0.29   0.288    1.45 0.010  0.236   
seqRun                 4      1.36   0.339    1.71 0.045  0.849   
Age                    1      0.66   0.663    3.33 0.022  0.006 **
Parity                 1      0.41   0.411    2.07 0.014  0.976   
BMI                    1      0.51   0.514    2.58 0.017  0.818   
MOD_Time_Interaction   1      0.13   0.129    0.65 0.004  1.000   
Residuals            119     23.67   0.199         0.790  0.293   
Total                133     29.97                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.6.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.17   0.585    2.94 0.039  0.098 . 
T1Dstatus              1      0.77   0.769    3.86 0.026  0.020 * 
MOD                    2      0.99   0.496    2.50 0.033  0.299   
Days                   1      0.29   0.288    1.45 0.010  0.191   
seqRun                 4      1.36   0.339    1.71 0.045  0.850   
Age                    1      0.66   0.663    3.33 0.022  0.005 **
Parity                 1      0.41   0.411    2.07 0.014  0.979   
BMI                    1      0.51   0.514    2.58 0.017  0.829   
MOD_Time_Interaction   1      0.13   0.132    0.67 0.004  1.000   
Residuals            119     23.67   0.199         0.790  0.306   
Total                133     29.97                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.6.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days        1      0.32   0.318    1.60 0.011  0.119   
seqRun      4      1.44   0.360    1.81 0.048  0.736   
Age         1      0.54   0.538    2.71 0.018  0.462   
Parity      1      0.54   0.537    2.71 0.018  0.365   
BMI         1      0.58   0.579    2.92 0.019  0.954   
HLA         2      1.07   0.537    2.71 0.036  0.135   
T1Dstatus   1      0.75   0.751    3.78 0.025  0.009 **
MOD         2      0.93   0.464    2.34 0.031  0.365   
Residuals 120     23.80   0.198         0.794  0.033 * 
Total     133     29.97                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.6.5 Mode of delivery (no interaction: T1)

Call:
adonis(formula = D ~ SeqRun + Nulliparous + BMI_conception +      T1Dstatus + Age_LMP + HLA.6DRML + MOD, data = Meta_df) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3      0.55   0.184   0.822 0.110  0.848  
Nulliparous     1      0.33   0.329   1.471 0.066  0.085 .
BMI_conception  1      0.26   0.263   1.177 0.053  0.262  
T1Dstatus       1      0.32   0.322   1.442 0.064  0.087 .
Age_LMP         1      0.19   0.188   0.841 0.038  0.689  
HLA.6DRML       2      0.33   0.167   0.748 0.067  0.889  
MOD             2      0.56   0.279   1.248 0.111  0.147  
Residuals      11      2.46   0.224         0.491         
Total          22      5.01                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.6.6 Mode of delivery (no interaction: T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1      0.30   0.296    1.60 0.032  0.537  
seqRun     3      1.05   0.351    1.89 0.115  0.463  
Age        1      0.29   0.289    1.56 0.032  0.461  
Parity     1      0.33   0.333    1.79 0.036  0.816  
BMI        1      0.22   0.220    1.19 0.024  0.892  
HLA        2      0.54   0.268    1.45 0.059  0.360  
T1Dstatus  1      0.36   0.364    1.97 0.040  0.062 .
MOD        2      0.49   0.247    1.33 0.054  0.510  
Residuals 30      5.56   0.185         0.608  0.222  
Total     42      9.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.6.7 Mode of delivery (no interaction: T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1      0.30   0.302   1.374 0.020  0.705  
seqRun     4      0.83   0.208   0.948 0.054  0.568  
Age        1      0.24   0.236   1.073 0.015  0.450  
Parity     1      0.27   0.274   1.245 0.018  0.505  
BMI        1      0.38   0.375   1.709 0.024  0.951  
HLA        2      0.48   0.239   1.089 0.031  0.425  
T1Dstatus  1      0.33   0.333   1.515 0.022  0.071 .
MOD        2      0.66   0.332   1.512 0.043  0.022 *
Residuals 54     11.86   0.220         0.772  0.068 .
Total     67     15.36                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.10.7 Carbohydrate intake

6.1.10.7.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      1.18   0.591    2.93 0.040  0.104  
T1Dstatus               1      0.79   0.790    3.91 0.027  0.016 *
Carbs                   1      0.46   0.455    2.26 0.015  0.487  
seqRun                  4      1.54   0.385    1.91 0.052  0.525  
Tri                     2      0.39   0.193    0.95 0.013  0.568  
Age                     1      0.53   0.532    2.64 0.018  0.470  
Parity                  1      0.45   0.452    2.24 0.015  0.926  
BMI                     1      0.54   0.544    2.70 0.018  0.624  
Carb_Time_Interaction   1      0.10   0.098    0.49 0.003  0.997  
Residuals             117     23.61   0.202         0.798  0.072 .
Total                 131     29.58                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.7.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      1.18   0.591    2.93 0.040  0.090 .
T1Dstatus               1      0.79   0.790    3.91 0.027  0.016 *
Carbs                   1      0.46   0.455    2.25 0.015  0.463  
seqRun                  4      1.54   0.385    1.90 0.052  0.507  
Tri                     2      0.39   0.193    0.95 0.013  0.515  
Age                     1      0.53   0.532    2.64 0.018  0.462  
Parity                  1      0.45   0.452    2.24 0.015  0.937  
BMI                     1      0.54   0.544    2.69 0.018  0.645  
Carb_Time_Interaction   1      0.08   0.077    0.38 0.003  1.000  
Residuals             117     23.63   0.202         0.799  0.131  
Total                 131     29.58                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.7.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      1.18   0.591    2.93 0.040  0.104  
T1Dstatus               1      0.79   0.790    3.91 0.027  0.015 *
Carbs                   1      0.46   0.455    2.26 0.015  0.500  
seqRun                  4      1.54   0.385    1.91 0.052  0.510  
Tri                     2      0.39   0.193    0.95 0.013  0.543  
Age                     1      0.53   0.532    2.64 0.018  0.491  
Parity                  1      0.45   0.452    2.24 0.015  0.931  
BMI                     1      0.54   0.544    2.70 0.018  0.620  
Carb_Time_Interaction   1      0.09   0.092    0.46 0.003  1.000  
Residuals             117     23.61   0.202         0.798  0.103  
Total                 131     29.58                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.7.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun      4      1.53   0.383    1.91 0.052  0.501  
Tri         2      0.43   0.216    1.08 0.015  0.420  
Age         1      0.55   0.552    2.75 0.019  0.430  
Parity      1      0.54   0.541    2.69 0.018  0.550  
BMI         1      0.56   0.556    2.77 0.019  0.990  
HLA         2      1.07   0.536    2.67 0.036  0.162  
T1Dstatus   1      0.78   0.776    3.86 0.026  0.013 *
Carbs       1      0.42   0.415    2.07 0.014  0.513  
Residuals 118     23.71   0.201         0.801  0.027 *
Total     131     29.58                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.10.8 Fibre intake

6.1.10.8.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      1.18   0.591    2.93 0.040  0.093 .
T1Dstatus                1      0.79   0.790    3.91 0.027  0.013 *
Fiber                    1      0.43   0.426    2.11 0.014  0.598  
seqRun                   4      1.52   0.381    1.89 0.051  0.577  
Tri                      2      0.39   0.195    0.97 0.013  0.514  
Age                      1      0.57   0.568    2.81 0.019  0.197  
Parity                   1      0.47   0.470    2.33 0.016  0.893  
BMI                      1      0.52   0.521    2.58 0.018  0.774  
Fiber_Time_Interaction   1      0.11   0.112    0.56 0.004  0.834  
Residuals              117     23.60   0.202         0.798  0.060 .
Total                  131     29.58                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.8.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      1.18   0.591    2.92 0.040  0.090 .
T1Dstatus                1      0.79   0.790    3.91 0.027  0.017 *
Fiber                    1      0.43   0.426    2.11 0.014  0.594  
seqRun                   4      1.52   0.381    1.88 0.051  0.558  
Tri                      2      0.39   0.195    0.97 0.013  0.512  
Age                      1      0.57   0.568    2.81 0.019  0.211  
Parity                   1      0.47   0.470    2.32 0.016  0.894  
BMI                      1      0.52   0.521    2.58 0.018  0.754  
Fiber_Time_Interaction   1      0.06   0.063    0.31 0.002  1.000  
Residuals              117     23.65   0.202         0.799  0.107  
Total                  131     29.58                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.8.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      1.18   0.591    2.93 0.040  0.094 .
T1Dstatus                1      0.79   0.790    3.92 0.027  0.022 *
Fiber                    1      0.43   0.426    2.11 0.014  0.587  
seqRun                   4      1.52   0.381    1.89 0.051  0.556  
Tri                      2      0.39   0.195    0.97 0.013  0.507  
Age                      1      0.57   0.568    2.81 0.019  0.213  
Parity                   1      0.47   0.470    2.33 0.016  0.878  
BMI                      1      0.52   0.521    2.58 0.018  0.744  
Fiber_Time_Interaction   1      0.12   0.116    0.57 0.004  1.000  
Residuals              117     23.60   0.202         0.798  0.133  
Total                  131     29.58                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.8.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun      4      1.53   0.383    1.91 0.052  0.500  
Tri         2      0.43   0.216    1.07 0.015  0.446  
Age         1      0.55   0.552    2.75 0.019  0.434  
Parity      1      0.54   0.541    2.69 0.018  0.539  
BMI         1      0.56   0.556    2.77 0.019  0.984  
HLA         2      1.07   0.536    2.67 0.036  0.163  
T1Dstatus   1      0.78   0.776    3.86 0.026  0.015 *
Fiber       1      0.41   0.407    2.02 0.014  0.573  
Residuals 118     23.71   0.201         0.802  0.062 .
Total     131     29.58                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

6.1.10.9 1,5-AG (glucose control measurement)

6.1.10.9.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.36   0.680    3.49 0.053  0.020 * 
T1Dstatus              1      0.73   0.730    3.75 0.029  0.039 * 
Days                   1      0.25   0.246    1.26 0.010  0.422   
seqRun                 3      1.32   0.441    2.26 0.052  0.808   
Age                    1      0.56   0.556    2.85 0.022  0.129   
Parity                 1      0.46   0.463    2.38 0.018  0.857   
BMI                    1      0.36   0.361    1.85 0.014  0.902   
AG15                   1      0.58   0.582    2.99 0.023  0.013 * 
AG15_T1D_Interaction   1      0.37   0.367    1.88 0.014  0.554   
Residuals            100     19.47   0.195         0.765  0.004 **
Total                112     25.45                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
6.1.10.9.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2      1.01   0.504    2.88 0.091   0.24
Days       1      0.18   0.180    1.03 0.016   0.60
seqRun     3      1.30   0.435    2.48 0.117   0.81
Age        1      0.39   0.389    2.22 0.035   0.79
Parity     1      0.59   0.592    3.38 0.053   0.49
BMI        1      0.46   0.463    2.64 0.042   0.17
AG15       1      0.35   0.350    2.00 0.031   0.85
Residuals 39      6.83   0.175         0.615   0.38
Total     49     11.12                 1.000       
6.1.10.9.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.25   0.625    3.56 0.092  0.075 .
Days       1      0.28   0.278    1.58 0.020  0.084 .
seqRun     3      1.16   0.385    2.19 0.085  0.954  
Age        1      0.67   0.674    3.84 0.049  0.015 *
Parity     1      0.46   0.458    2.61 0.034  0.761  
BMI        1      0.16   0.161    0.92 0.012  1.000  
AG15       1      0.56   0.555    3.16 0.041  0.868  
Residuals 52      9.13   0.176         0.668  0.293  
Total     62     13.66                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7 Strain taxonomic level

7.1 Microbial community composition analysis at strain level (Beta diversity analysis)

7.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
seqRun                 4      1.41   0.352    1.66 0.045  0.485   
Days                   1      0.33   0.326    1.54 0.010  0.062 . 
T1D_Time_Interaction   1      0.81   0.809    3.81 0.026  0.003 **
Age                    1      0.55   0.547    2.58 0.017  0.510   
Parity                 1      0.58   0.583    2.75 0.019  0.436   
BMI                    1      0.49   0.491    2.32 0.016  0.998   
HLA                    2      1.33   0.663    3.12 0.042  0.020 * 
T1Dstatus              1      0.35   0.345    1.63 0.011  0.831   
Residuals            121     25.66   0.212         0.815  0.051 . 
Total                133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.003

7.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3      0.54   0.179   0.718 0.100   0.96
Nulliparous     1      0.33   0.326   1.308 0.061   0.14
Age_LMP         1      0.26   0.255   1.024 0.048   0.44
BMI_conception  1      0.28   0.282   1.129 0.053   0.29
HLA.6DRML       2      0.38   0.191   0.764 0.071   0.87
T1Dstatus       1      0.33   0.329   1.320 0.062   0.14
Residuals      13      3.24   0.249         0.606       
Total          22      5.35                 1.000       
[1] 0.135

Beta diversity Plot

7.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3      1.04   0.347    1.77 0.109  0.001 ***
Age        1      0.30   0.299    1.53 0.031  0.480    
Parity     1      0.36   0.360    1.83 0.038  0.001 ***
BMI        1      0.20   0.204    1.04 0.021  0.510    
HLA        2      0.77   0.384    1.96 0.080  0.043 *  
T1Dstatus  1      0.42   0.424    2.16 0.044  0.042 *  
Residuals 33      6.47   0.196         0.676  0.007 ** 
Total     42      9.57                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

7.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
seqRun     4      0.87   0.217   0.929 0.054  0.481   
Age        1      0.23   0.227   0.972 0.014  0.397   
Parity     1      0.27   0.271   1.164 0.017  0.603   
BMI        1      0.37   0.374   1.604 0.023  0.747   
HLA        2      0.54   0.271   1.162 0.034  0.295   
T1Dstatus  1      0.50   0.503   2.158 0.031  0.003 **
Residuals 57     13.29   0.233         0.827  0.063 . 
Total     67     16.07                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

7.1.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.04   0.521    2.77 0.069  0.193  
seqRun     3      1.21   0.405    2.15 0.080  0.882  
Age        1      0.43   0.427    2.27 0.028  0.951  
Parity     1      0.63   0.626    3.32 0.041  0.071 .
BMI        1      0.67   0.669    3.55 0.044  0.573  
Days       1      0.24   0.239    1.27 0.016  0.055 .
Residuals 58     10.93   0.188         0.722  0.177  
Total     67     15.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

7.1.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.04   0.521    2.76 0.069  0.189  
seqRun     3      1.21   0.405    2.14 0.080  0.871  
Age        1      0.43   0.427    2.26 0.028  0.947  
Parity     1      0.63   0.626    3.31 0.041  0.059 .
BMI        1      0.67   0.669    3.54 0.044  0.577  
Tri        2      0.39   0.196    1.04 0.026  0.045 *
Residuals 57     10.78   0.189         0.711  0.138  
Total     67     15.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

7.1.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.38   0.689    3.39 0.089  0.047 *
seqRun     4      1.38   0.344    1.69 0.089  0.993  
Age        1      0.62   0.619    3.05 0.040  0.019 *
Parity     1      0.50   0.502    2.47 0.032  0.719  
BMI        1      0.21   0.212    1.04 0.014  0.998  
Days       1      0.25   0.252    1.24 0.016  0.159  
Residuals 55     11.18   0.203         0.720  0.135  
Total     65     15.52                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

7.1.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.38   0.689    3.36 0.089  0.036 *
seqRun     4      1.38   0.344    1.68 0.089  0.988  
Age        1      0.62   0.619    3.02 0.040  0.020 *
Parity     1      0.50   0.502    2.45 0.032  0.730  
BMI        1      0.21   0.212    1.03 0.014  0.997  
Tri        2      0.35   0.177    0.86 0.023  0.500  
Residuals 54     11.07   0.205         0.714  0.162  
Total     65     15.52                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

7.1.9 Other factors

7.1.9.1 Age at conception

7.1.9.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.39   0.696    3.26 0.044  0.020 * 
T1Dstatus              1      0.90   0.904    4.23 0.029  0.009 **
seqRun                 4      1.41   0.353    1.65 0.045  0.608   
Tri                    2      0.43   0.217    1.01 0.014  0.473   
Age                    1      0.57   0.566    2.65 0.018  0.322   
Parity                 1      0.50   0.496    2.32 0.016  0.929   
BMI                    1      0.51   0.506    2.37 0.016  0.916   
Age_Time_Interaction   1      0.16   0.157    0.73 0.005  0.381   
Residuals            120     25.63   0.214         0.814  0.009 **
Total                133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.39   0.696    3.25 0.044  0.022 * 
T1Dstatus              1      0.90   0.904    4.22 0.029  0.004 **
seqRun                 4      1.41   0.353    1.65 0.045  0.630   
Tri                    2      0.43   0.217    1.01 0.014  0.487   
Age                    1      0.57   0.566    2.64 0.018  0.332   
Parity                 1      0.50   0.496    2.32 0.016  0.930   
BMI                    1      0.51   0.506    2.36 0.016  0.918   
Age_Time_Interaction   1      0.10   0.099    0.46 0.003  0.539   
Residuals            120     25.69   0.214         0.816  0.007 **
Total                133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.39   0.696    3.26 0.044  0.020 * 
T1Dstatus              1      0.90   0.904    4.23 0.029  0.007 **
seqRun                 4      1.41   0.353    1.65 0.045  0.596   
Tri                    2      0.43   0.217    1.01 0.014  0.467   
Age                    1      0.57   0.566    2.65 0.018  0.312   
Parity                 1      0.50   0.496    2.32 0.016  0.921   
BMI                    1      0.51   0.506    2.36 0.016  0.914   
Age_Time_Interaction   1      0.12   0.123    0.57 0.004  0.587   
Residuals            120     25.67   0.214         0.815  0.005 **
Total                133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.1.4 Age at conception (no interaction and within trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2      0.55   0.275   1.103 0.103   0.23
T1Dstatus  1      0.26   0.263   1.054 0.049   0.35
seqRun     3      0.49   0.163   0.652 0.091   0.95
Parity     1      0.31   0.308   1.235 0.058   0.57
BMI        1      0.32   0.322   1.289 0.060   0.19
Age        1      0.18   0.180   0.722 0.034   0.92
Residuals 13      3.24   0.249         0.606   0.58
Total     22      5.35                 1.000       
7.1.9.1.5 Age at conception (no interaction and within trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.82   0.410    2.09 0.086  0.038 * 
T1Dstatus  1      0.52   0.520    2.65 0.054  0.018 * 
seqRun     3      0.92   0.307    1.57 0.096  0.777   
Parity     1      0.31   0.312    1.59 0.033  0.875   
BMI        1      0.21   0.214    1.09 0.022  0.485   
Age        1      0.31   0.310    1.58 0.032  0.287   
Residuals 33      6.47   0.196         0.676  0.009 **
Total     42      9.57                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.1.6 Age at conception (no interaction and within trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.65   0.324   1.390 0.040  0.066 . 
T1Dstatus  1      0.48   0.481   2.064 0.030  0.004 **
seqRun     4      0.86   0.215   0.921 0.053  0.813   
Parity     1      0.26   0.260   1.116 0.016  0.732   
BMI        1      0.31   0.309   1.325 0.019  0.988   
Age        1      0.23   0.226   0.970 0.014  0.375   
Residuals 57     13.29   0.233         0.827  0.057 . 
Total     67     16.07                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.2 Body max index (BMI)

7.1.9.2.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.39   0.696    3.26 0.044  0.022 * 
T1Dstatus              1      0.90   0.904    4.23 0.029  0.005 **
seqRun                 4      1.41   0.353    1.65 0.045  0.597   
Tri                    2      0.43   0.217    1.01 0.014  0.459   
Age                    1      0.57   0.566    2.65 0.018  0.296   
Parity                 1      0.50   0.496    2.32 0.016  0.925   
BMI                    1      0.51   0.506    2.36 0.016  0.914   
BMI_Time_Interaction   1      0.13   0.134    0.63 0.004  0.394   
Residuals            120     25.66   0.214         0.814  0.003 **
Total                133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.2.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.39   0.696    3.25 0.044  0.031 * 
T1Dstatus              1      0.90   0.904    4.23 0.029  0.007 **
seqRun                 4      1.41   0.353    1.65 0.045  0.614   
Tri                    2      0.43   0.217    1.01 0.014  0.450   
Age                    1      0.57   0.566    2.65 0.018  0.286   
Parity                 1      0.50   0.496    2.32 0.016  0.915   
BMI                    1      0.51   0.506    2.36 0.016  0.925   
BMI_Time_Interaction   1      0.12   0.117    0.55 0.004  0.889   
Residuals            120     25.67   0.214         0.815  0.007 **
Total                133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.2.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.39   0.696    3.27 0.044  0.021 * 
T1Dstatus              1      0.90   0.904    4.24 0.029  0.003 **
seqRun                 4      1.41   0.353    1.66 0.045  0.629   
Tri                    2      0.43   0.217    1.02 0.014  0.473   
Age                    1      0.57   0.566    2.66 0.018  0.295   
Parity                 1      0.50   0.496    2.33 0.016  0.927   
BMI                    1      0.51   0.506    2.37 0.016  0.927   
BMI_Time_Interaction   1      0.22   0.217    1.02 0.007  0.105   
Residuals            120     25.57   0.213         0.812  0.002 **
Total                133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.2.4 BMI (no interaction but within T1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2      0.55   0.275   1.152 0.103   0.25
T1Dstatus  1      0.26   0.263   1.101 0.049   0.35
seqRun     1      0.22   0.224   0.938 0.042   0.61
Age        1      0.23   0.233   0.974 0.043   0.87
Parity     1      0.27   0.266   1.114 0.050   0.74
BMI        1      0.23   0.234   0.979 0.044   0.69
Residuals 15      3.58   0.239         0.669   0.54
Total     22      5.35                 1.000       
7.1.9.2.5 BMI (no interaction but within T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.82   0.410    2.04 0.086  0.042 * 
T1Dstatus  1      0.52   0.520    2.59 0.054  0.012 * 
seqRun     1      0.40   0.402    2.01 0.042  0.907   
Age        1      0.31   0.309    1.54 0.032  0.302   
Parity     1      0.31   0.307    1.53 0.032  0.875   
BMI        1      0.20   0.205    1.02 0.021  0.395   
Residuals 35      7.01   0.200         0.732  0.010 **
Total     42      9.57                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.2.6 BMI (no interaction but within T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.65   0.324   1.392 0.040  0.066 . 
T1Dstatus  1      0.48   0.481   2.067 0.030  0.002 **
seqRun     1      0.17   0.166   0.713 0.010  0.033 * 
Age        1      0.25   0.250   1.074 0.016  0.565   
Parity     1      0.26   0.256   1.099 0.016  0.632   
BMI        1      0.30   0.305   1.309 0.019  0.977   
Residuals 60     13.97   0.233         0.869  0.006 **
Total     67     16.07                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.3 HLA type

7.1.9.3.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.39   0.696    3.27 0.044  0.025 * 
T1Dstatus              1      0.90   0.904    4.25 0.029  0.006 **
Days                   1      0.33   0.335    1.57 0.011  0.173   
seqRun                 4      1.37   0.344    1.62 0.044  0.544   
Age                    1      0.56   0.559    2.63 0.018  0.336   
Parity                 1      0.51   0.509    2.39 0.016  0.862   
BMI                    1      0.49   0.494    2.32 0.016  0.918   
HLA_Time_Interaction   1      0.20   0.196    0.92 0.006  1.000   
Residuals            121     25.74   0.213         0.817  0.068 . 
Total                133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.3.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.39   0.696    3.26 0.044  0.036 * 
T1Dstatus              1      0.90   0.904    4.24 0.029  0.007 **
Days                   1      0.33   0.335    1.57 0.011  0.160   
seqRun                 4      1.37   0.344    1.61 0.044  0.545   
Age                    1      0.56   0.559    2.62 0.018  0.348   
Parity                 1      0.51   0.509    2.38 0.016  0.878   
BMI                    1      0.49   0.494    2.31 0.016  0.916   
HLA_Time_Interaction   1      0.12   0.121    0.57 0.004  1.000   
Residuals            121     25.81   0.213         0.819  0.101   
Total                133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.3.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.39   0.696    3.27 0.044  0.032 * 
T1Dstatus              1      0.90   0.904    4.25 0.029  0.007 **
Days                   1      0.33   0.335    1.57 0.011  0.173   
seqRun                 4      1.37   0.344    1.61 0.044  0.547   
Age                    1      0.56   0.559    2.62 0.018  0.347   
Parity                 1      0.51   0.509    2.39 0.016  0.902   
BMI                    1      0.49   0.494    2.32 0.016  0.922   
HLA_Time_Interaction   1      0.16   0.159    0.75 0.005  1.000   
Residuals            121     25.77   0.213         0.818  0.030 * 
Total                133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.3.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days        1      0.38   0.383    1.80 0.012  0.034 * 
seqRun      4      1.35   0.338    1.59 0.043  0.664   
Age         1      0.55   0.550    2.59 0.017  0.492   
Parity      1      0.58   0.578    2.72 0.018  0.272   
BMI         1      0.55   0.553    2.60 0.018  0.971   
T1Dstatus   1      0.80   0.797    3.75 0.025  0.019 * 
HLA         2      1.35   0.677    3.19 0.043  0.026 * 
Residuals 122     25.93   0.213         0.823  0.002 **
Total     133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.4 Parity

7.1.9.4.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                         Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
HLA                       2      1.39   0.696    3.27 0.044  0.023 *  
T1Dstatus                 1      0.90   0.904    4.25 0.029  0.007 ** 
Days                      1      0.33   0.335    1.57 0.011  0.134    
seqRun                    4      1.37   0.344    1.61 0.044  0.524    
Age                       1      0.56   0.559    2.63 0.018  0.366    
Parity                    1      0.51   0.509    2.39 0.016  0.885    
BMI                       1      0.49   0.494    2.32 0.016  0.912    
Parity_Time_Interaction   1      0.19   0.190    0.89 0.006  0.087 .  
Residuals               121     25.74   0.213         0.817  0.001 ***
Total                   133     31.50                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.4.2 Parity (no interaction but within T1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2      0.55   0.275   1.152 0.103   0.24
T1Dstatus  1      0.26   0.263   1.101 0.049   0.34
seqRun     1      0.22   0.224   0.938 0.042   0.58
Age        1      0.23   0.233   0.974 0.043   0.85
BMI        1      0.25   0.246   1.031 0.046   0.87
Parity     1      0.25   0.254   1.063 0.047   0.48
Residuals 15      3.58   0.239         0.669   0.53
Total     22      5.35                 1.000       
7.1.9.4.3 Parity (no interaction but within T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.82   0.410    2.04 0.086  0.050 * 
T1Dstatus  1      0.52   0.520    2.59 0.054  0.014 * 
seqRun     1      0.40   0.402    2.01 0.042  0.875   
Age        1      0.31   0.309    1.54 0.032  0.299   
BMI        1      0.28   0.281    1.40 0.029  0.298   
Parity     1      0.23   0.231    1.15 0.024  0.958   
Residuals 35      7.01   0.200         0.732  0.010 **
Total     42      9.57                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.4.4 Parity (no interaction but within T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA        2      0.65   0.324   1.392 0.040  0.073 . 
T1Dstatus  1      0.48   0.481   2.067 0.030  0.009 **
seqRun     1      0.17   0.166   0.713 0.010  0.029 * 
Age        1      0.25   0.250   1.074 0.016  0.573   
BMI        1      0.30   0.305   1.309 0.019  0.980   
Parity     1      0.26   0.256   1.099 0.016  0.731   
Residuals 60     13.97   0.233         0.869  0.005 **
Total     67     16.07                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.5 Mode of delivery

7.1.9.5.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
HLA                    2      1.39   0.696    3.36 0.044  0.022 *  
T1Dstatus              1      0.90   0.904    4.36 0.029  0.004 ** 
MOD                    2      1.00   0.501    2.42 0.032  0.401    
Days                   1      0.34   0.344    1.66 0.011  0.116    
seqRun                 4      1.33   0.332    1.60 0.042  0.708    
Age                    1      0.74   0.741    3.57 0.024  0.001 ***
Parity                 1      0.42   0.419    2.02 0.013  0.987    
BMI                    1      0.48   0.479    2.31 0.015  0.902    
MOD_Time_Interaction   1      0.20   0.204    0.98 0.006  1.000    
Residuals            119     24.69   0.207         0.784  0.022 *  
Total                133     31.50                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.5.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.39   0.696    3.35 0.044  0.025 * 
T1Dstatus              1      0.90   0.904    4.34 0.029  0.006 **
MOD                    2      1.00   0.501    2.41 0.032  0.400   
Days                   1      0.34   0.344    1.65 0.011  0.104   
seqRun                 4      1.33   0.332    1.59 0.042  0.727   
Age                    1      0.74   0.741    3.56 0.024  0.003 **
Parity                 1      0.42   0.419    2.01 0.013  0.989   
BMI                    1      0.48   0.479    2.30 0.015  0.909   
MOD_Time_Interaction   1      0.12   0.123    0.59 0.004  1.000   
Residuals            119     24.77   0.208         0.786  0.078 . 
Total                133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.5.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
HLA                    2      1.39   0.696    3.35 0.044  0.022 *  
T1Dstatus              1      0.90   0.904    4.34 0.029  0.002 ** 
MOD                    2      1.00   0.501    2.41 0.032  0.416    
Days                   1      0.34   0.344    1.65 0.011  0.105    
seqRun                 4      1.33   0.332    1.59 0.042  0.735    
Age                    1      0.74   0.741    3.56 0.024  0.001 ***
Parity                 1      0.42   0.419    2.01 0.013  0.986    
BMI                    1      0.48   0.479    2.30 0.015  0.885    
MOD_Time_Interaction   1      0.12   0.123    0.59 0.004  1.000    
Residuals            119     24.77   0.208         0.786  0.111    
Total                133     31.50                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.5.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days        1      0.38   0.383    1.84 0.012  0.042 * 
seqRun      4      1.35   0.338    1.63 0.043  0.664   
Age         1      0.55   0.550    2.65 0.017  0.490   
Parity      1      0.58   0.578    2.79 0.018  0.276   
BMI         1      0.55   0.553    2.67 0.018  0.965   
HLA         2      1.28   0.638    3.08 0.040  0.048 * 
T1Dstatus   1      0.88   0.876    4.22 0.028  0.007 **
MOD         2      1.04   0.521    2.51 0.033  0.277   
Residuals 120     24.89   0.207         0.790  0.002 **
Total     133     31.50                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.6 Carbohydrate intake

7.1.9.6.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
HLA                     2      1.40   0.699    3.29 0.045  0.039 *  
T1Dstatus               1      0.93   0.929    4.37 0.030  0.001 ***
Carbs                   1      0.42   0.423    1.99 0.014  0.684    
seqRun                  4      1.45   0.362    1.70 0.047  0.611    
Tri                     2      0.43   0.216    1.02 0.014  0.390    
Age                     1      0.52   0.524    2.46 0.017  0.670    
Parity                  1      0.47   0.471    2.22 0.015  0.946    
BMI                     1      0.52   0.516    2.43 0.017  0.737    
Carb_Time_Interaction   1      0.10   0.100    0.47 0.003  0.994    
Residuals             117     24.87   0.213         0.799  0.036 *  
Total                 131     31.11                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.6.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                     2      1.40   0.699    3.29 0.045  0.017 * 
T1Dstatus               1      0.93   0.929    4.37 0.030  0.007 **
Carbs                   1      0.42   0.423    1.99 0.014  0.650   
seqRun                  4      1.45   0.362    1.70 0.047  0.620   
Tri                     2      0.43   0.216    1.02 0.014  0.404   
Age                     1      0.52   0.524    2.46 0.017  0.634   
Parity                  1      0.47   0.471    2.22 0.015  0.954   
BMI                     1      0.52   0.516    2.43 0.017  0.752   
Carb_Time_Interaction   1      0.10   0.097    0.46 0.003  1.000   
Residuals             117     24.87   0.213         0.799  0.047 * 
Total                 131     31.11                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.6.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                     2      1.40   0.699    3.29 0.045  0.022 * 
T1Dstatus               1      0.93   0.929    4.37 0.030  0.004 **
Carbs                   1      0.42   0.423    1.99 0.014  0.677   
seqRun                  4      1.45   0.362    1.70 0.047  0.596   
Tri                     2      0.43   0.216    1.02 0.014  0.396   
Age                     1      0.52   0.524    2.46 0.017  0.670   
Parity                  1      0.47   0.471    2.22 0.015  0.953   
BMI                     1      0.52   0.516    2.43 0.017  0.760   
Carb_Time_Interaction   1      0.10   0.105    0.49 0.003  0.996   
Residuals             117     24.86   0.213         0.799  0.036 * 
Total                 131     31.11                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.6.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
seqRun      4      1.45   0.363    1.71 0.047  0.495   
Tri         2      0.48   0.240    1.13 0.015  0.260   
Age         1      0.57   0.566    2.67 0.018  0.446   
Parity      1      0.58   0.580    2.74 0.019  0.464   
BMI         1      0.54   0.544    2.57 0.017  0.949   
HLA         2      1.28   0.639    3.02 0.041  0.046 * 
T1Dstatus   1      0.91   0.908    4.29 0.029  0.005 **
Carbs       1      0.34   0.336    1.59 0.011  0.856   
Residuals 118     24.97   0.212         0.803  0.015 * 
Total     131     31.11                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.7 Fibre intake

7.1.9.7.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                      2      1.40   0.699    3.30 0.045  0.022 * 
T1Dstatus                1      0.93   0.929    4.38 0.030  0.007 **
Fiber                    1      0.42   0.421    1.98 0.014  0.682   
seqRun                   4      1.42   0.354    1.67 0.046  0.734   
Tri                      2      0.44   0.219    1.03 0.014  0.357   
Age                      1      0.55   0.553    2.60 0.018  0.446   
Parity                   1      0.50   0.496    2.34 0.016  0.914   
BMI                      1      0.51   0.509    2.40 0.016  0.782   
Fiber_Time_Interaction   1      0.12   0.115    0.54 0.004  0.795   
Residuals              117     24.83   0.212         0.798  0.009 **
Total                  131     31.11                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.7.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                      2      1.40   0.699    3.29 0.045  0.014 * 
T1Dstatus                1      0.93   0.929    4.37 0.030  0.009 **
Fiber                    1      0.42   0.421    1.98 0.014  0.675   
seqRun                   4      1.42   0.354    1.67 0.046  0.744   
Tri                      2      0.44   0.219    1.03 0.014  0.316   
Age                      1      0.55   0.553    2.60 0.018  0.436   
Parity                   1      0.50   0.496    2.33 0.016  0.895   
BMI                      1      0.51   0.509    2.39 0.016  0.795   
Fiber_Time_Interaction   1      0.07   0.069    0.32 0.002  1.000   
Residuals              117     24.88   0.213         0.800  0.026 * 
Total                  131     31.11                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.7.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                      2      1.40   0.699    3.29 0.045  0.025 * 
T1Dstatus                1      0.93   0.929    4.37 0.030  0.004 **
Fiber                    1      0.42   0.421    1.98 0.014  0.680   
seqRun                   4      1.42   0.354    1.67 0.046  0.731   
Tri                      2      0.44   0.219    1.03 0.014  0.357   
Age                      1      0.55   0.553    2.60 0.018  0.446   
Parity                   1      0.50   0.496    2.34 0.016  0.892   
BMI                      1      0.51   0.509    2.40 0.016  0.776   
Fiber_Time_Interaction   1      0.10   0.105    0.49 0.003  1.000   
Residuals              117     24.84   0.212         0.799  0.033 * 
Total                  131     31.11                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.7.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
seqRun      4      1.45   0.363    1.72 0.047  0.609   
Tri         2      0.48   0.240    1.14 0.015  0.282   
Age         1      0.57   0.566    2.68 0.018  0.465   
Parity      1      0.58   0.580    2.74 0.019  0.462   
BMI         1      0.54   0.544    2.57 0.017  0.954   
HLA         2      1.28   0.639    3.02 0.041  0.045 * 
T1Dstatus   1      0.91   0.908    4.29 0.029  0.002 **
Fiber       1      0.36   0.356    1.68 0.011  0.835   
Residuals 118     24.95   0.211         0.802  0.013 * 
Total     131     31.11                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

7.1.9.8 1,5-AG (glucose control measurement)

7.1.9.8.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      1.60   0.799    3.90 0.060  0.004 **
T1Dstatus              1      0.84   0.841    4.10 0.031  0.015 * 
Days                   1      0.29   0.287    1.40 0.011  0.230   
seqRun                 3      1.24   0.413    2.02 0.046  0.920   
Age                    1      0.57   0.573    2.80 0.021  0.114   
Parity                 1      0.46   0.464    2.26 0.017  0.875   
BMI                    1      0.36   0.361    1.76 0.013  0.928   
AG15                   1      0.55   0.554    2.70 0.021  0.021 * 
AG15_T1D_Interaction   1      0.33   0.335    1.63 0.013  0.960   
Residuals            100     20.49   0.205         0.766  0.002 **
Total                112     26.74                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.8.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.16   0.581    3.21 0.101  0.092 .
Days       1      0.21   0.210    1.16 0.018  0.364  
seqRun     3      1.23   0.411    2.27 0.107  0.890  
Age        1      0.39   0.385    2.13 0.033  0.880  
Parity     1      0.61   0.614    3.40 0.053  0.390  
BMI        1      0.48   0.483    2.67 0.042  0.188  
AG15       1      0.38   0.384    2.12 0.033  0.895  
Residuals 39      7.05   0.181         0.612  0.227  
Total     49     11.52                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
7.1.9.8.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      1.36   0.682    3.63 0.095  0.058 .
Days       1      0.29   0.294    1.57 0.020  0.107  
seqRun     3      1.17   0.390    2.08 0.081  0.984  
Age        1      0.68   0.677    3.61 0.047  0.020 *
Parity     1      0.47   0.471    2.51 0.033  0.830  
BMI        1      0.18   0.182    0.97 0.013  1.000  
AG15       1      0.50   0.504    2.69 0.035  0.878  
Residuals 52      9.76   0.188         0.677  0.271  
Total     62     14.42                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8 Genus taxonomic level

8.1 Microbial community composition analysis at Genus level (Beta diversity analysis)

8.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
seqRun                 4      0.66   0.166    1.68 0.045  0.507   
Days                   1      0.20   0.203    2.05 0.014  0.158   
T1D_Time_Interaction   1      0.44   0.439    4.45 0.030  0.006 **
Age                    1      0.38   0.383    3.88 0.026  0.619   
Parity                 1      0.22   0.223    2.26 0.015  0.028 * 
BMI                    1      0.35   0.354    3.58 0.024  1.000   
HLA                    2      0.40   0.201    2.03 0.027  0.387   
T1Dstatus              1      0.12   0.120    1.22 0.008  0.786   
Residuals            121     11.95   0.099         0.811  0.444   
Total                133     14.74                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.006

8.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3     0.255  0.0848   0.750 0.101   0.80
Nulliparous     1     0.148  0.1483   1.311 0.059   0.22
Age_LMP         1     0.164  0.1637   1.448 0.065   0.17
BMI_conception  1     0.120  0.1202   1.063 0.048   0.38
HLA.6DRML       2     0.195  0.0976   0.863 0.077   0.65
T1Dstatus       1     0.169  0.1694   1.498 0.067   0.17
Residuals      13     1.470  0.1131         0.583       
Total          22     2.521                 1.000       
[1] 0.167

Beta diversity Plot

8.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3      0.67  0.2226    2.39 0.143  0.001 ***
Age        1      0.18  0.1810    1.94 0.039  0.675    
Parity     1      0.13  0.1256    1.35 0.027  0.001 ***
BMI        1      0.10  0.1002    1.08 0.021  0.648    
HLA        2      0.31  0.1570    1.69 0.067  0.198    
T1Dstatus  1      0.22  0.2164    2.32 0.046  0.085 .  
Residuals 33      3.07  0.0932         0.657  0.081 .  
Total     42      4.68                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

8.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
seqRun     4      0.31   0.078    0.73 0.043   0.50
Age        1      0.14   0.141    1.33 0.019   0.13
Parity     1      0.18   0.175    1.66 0.024   0.14
BMI        1      0.34   0.341    3.22 0.047   0.88
HLA        2      0.11   0.053    0.50 0.015   0.96
T1Dstatus  1      0.17   0.173    1.64 0.024   0.12
Residuals 57      6.04   0.106         0.829   0.83
Total     67      7.29                 1.000       

Beta diversity Plot

8.1.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.27   0.134    1.72 0.041  0.738  
seqRun     3      0.67   0.224    2.88 0.102  0.432  
Age        1      0.26   0.262    3.37 0.040  0.674  
Parity     1      0.17   0.170    2.19 0.026  0.119  
BMI        1      0.55   0.551    7.10 0.084  0.481  
Days       1      0.16   0.157    2.02 0.024  0.018 *
Residuals 58      4.50   0.078         0.684  0.395  
Total     67      6.58                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

8.1.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.27   0.134    1.71 0.041  0.785  
seqRun     3      0.67   0.224    2.86 0.102  0.400  
Age        1      0.26   0.262    3.35 0.040  0.656  
Parity     1      0.17   0.170    2.18 0.026  0.124  
BMI        1      0.55   0.551    7.05 0.084  0.493  
Tri        2      0.20   0.101    1.29 0.031  0.024 *
Residuals 57      4.46   0.078         0.677  0.348  
Total     67      6.58                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

8.1.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.66   0.329    3.14 0.085  0.129  
seqRun     4      0.47   0.117    1.12 0.061  0.994  
Age        1      0.50   0.505    4.82 0.065  0.017 *
Parity     1      0.11   0.112    1.07 0.015  0.959  
BMI        1      0.09   0.094    0.90 0.012  0.998  
Days       1      0.12   0.115    1.10 0.015  0.351  
Residuals 55      5.76   0.105         0.747  0.309  
Total     65      7.72                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

8.1.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.66   0.329    3.12 0.085  0.120  
seqRun     4      0.47   0.117    1.11 0.061  0.994  
Age        1      0.50   0.505    4.79 0.065  0.012 *
Parity     1      0.11   0.112    1.06 0.015  0.951  
BMI        1      0.09   0.094    0.89 0.012  0.998  
Tri        2      0.18   0.090    0.86 0.023  0.630  
Residuals 54      5.70   0.106         0.738  0.417  
Total     65      7.72                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

8.1.9 Other factors

8.1.9.1 Age at conception

8.1.9.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.236    2.37 0.032  0.341  
T1Dstatus              1      0.45   0.448    4.50 0.030  0.025 *
seqRun                 4      0.66   0.164    1.65 0.045  0.653  
Tri                    2      0.21   0.103    1.03 0.014  0.564  
Age                    1      0.41   0.410    4.12 0.028  0.312  
Parity                 1      0.17   0.172    1.73 0.012  0.918  
BMI                    1      0.37   0.366    3.67 0.025  0.934  
Age_Time_Interaction   1      0.06   0.063    0.63 0.004  0.630  
Residuals            120     11.95   0.100         0.810  0.294  
Total                133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.236    2.37 0.032  0.342  
T1Dstatus              1      0.45   0.448    4.49 0.030  0.033 *
seqRun                 4      0.66   0.164    1.65 0.045  0.649  
Tri                    2      0.21   0.103    1.03 0.014  0.566  
Age                    1      0.41   0.410    4.12 0.028  0.322  
Parity                 1      0.17   0.172    1.72 0.012  0.905  
BMI                    1      0.37   0.366    3.67 0.025  0.915  
Age_Time_Interaction   1      0.04   0.043    0.43 0.003  0.693  
Residuals            120     11.97   0.100         0.812  0.303  
Total                133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.236    2.38 0.032  0.362  
T1Dstatus              1      0.45   0.448    4.50 0.030  0.038 *
seqRun                 4      0.66   0.164    1.65 0.045  0.663  
Tri                    2      0.21   0.103    1.03 0.014  0.585  
Age                    1      0.41   0.410    4.13 0.028  0.328  
Parity                 1      0.17   0.172    1.73 0.012  0.929  
BMI                    1      0.37   0.366    3.68 0.025  0.904  
Age_Time_Interaction   1      0.07   0.072    0.73 0.005  0.368  
Residuals            120     11.94   0.099         0.810  0.291  
Total                133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.1.4 Age at conception (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      0.47   0.236    2.38 0.032  0.346  
T1Dstatus   1      0.45   0.448    4.51 0.030  0.045 *
seqRun      4      0.66   0.164    1.66 0.045  0.643  
Tri         2      0.21   0.103    1.04 0.014  0.549  
Parity      1      0.17   0.173    1.74 0.012  0.937  
BMI         1      0.36   0.364    3.66 0.025  0.900  
Age         1      0.41   0.412    4.15 0.028  0.331  
Residuals 121     12.01   0.099         0.815  0.278  
Total     133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.2 Body max index (BMI)

8.1.9.2.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.236    2.37 0.032  0.375  
T1Dstatus              1      0.45   0.448    4.49 0.030  0.029 *
seqRun                 4      0.66   0.164    1.65 0.045  0.640  
Tri                    2      0.21   0.103    1.03 0.014  0.553  
Age                    1      0.41   0.410    4.12 0.028  0.299  
Parity                 1      0.17   0.172    1.72 0.012  0.933  
BMI                    1      0.37   0.366    3.67 0.025  0.921  
BMI_Time_Interaction   1      0.04   0.041    0.41 0.003  0.829  
Residuals            120     11.97   0.100         0.812  0.315  
Total                133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.2.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.236    2.37 0.032  0.351  
T1Dstatus              1      0.45   0.448    4.49 0.030  0.025 *
seqRun                 4      0.66   0.164    1.65 0.045  0.636  
Tri                    2      0.21   0.103    1.03 0.014  0.548  
Age                    1      0.41   0.410    4.12 0.028  0.308  
Parity                 1      0.17   0.172    1.72 0.012  0.909  
BMI                    1      0.37   0.366    3.67 0.025  0.939  
BMI_Time_Interaction   1      0.05   0.050    0.50 0.003  0.629  
Residuals            120     11.96   0.100         0.811  0.277  
Total                133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.2.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.236    2.38 0.032  0.326  
T1Dstatus              1      0.45   0.448    4.51 0.030  0.028 *
seqRun                 4      0.66   0.164    1.66 0.045  0.660  
Tri                    2      0.21   0.103    1.04 0.014  0.557  
Age                    1      0.41   0.410    4.14 0.028  0.341  
Parity                 1      0.17   0.172    1.73 0.012  0.922  
BMI                    1      0.37   0.366    3.69 0.025  0.935  
BMI_Time_Interaction   1      0.11   0.106    1.06 0.007  0.242  
Residuals            120     11.90   0.099         0.808  0.231  
Total                133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.2.4 BMI (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      0.47   0.236    2.38 0.032  0.346  
T1Dstatus   1      0.45   0.448    4.51 0.030  0.029 *
seqRun      4      0.66   0.164    1.66 0.045  0.655  
Tri         2      0.21   0.103    1.04 0.014  0.559  
Age         1      0.41   0.410    4.14 0.028  0.303  
Parity      1      0.17   0.172    1.73 0.012  0.913  
BMI         1      0.37   0.366    3.69 0.025  0.925  
Residuals 121     12.01   0.099         0.815  0.272  
Total     133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.3 HLA type

8.1.9.3.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.236    2.39 0.032  0.360  
T1Dstatus              1      0.45   0.448    4.52 0.030  0.036 *
Days                   1      0.24   0.242    2.44 0.016  0.130  
seqRun                 4      0.61   0.152    1.53 0.041  0.667  
Age                    1      0.40   0.398    4.01 0.027  0.323  
Parity                 1      0.18   0.176    1.78 0.012  0.903  
BMI                    1      0.35   0.351    3.54 0.024  0.939  
HLA_Time_Interaction   1      0.06   0.062    0.63 0.004  1.000  
Residuals            121     11.99   0.099         0.813  0.430  
Total                133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.3.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.236    2.39 0.032  0.346  
T1Dstatus              1      0.45   0.448    4.52 0.030  0.033 *
Days                   1      0.24   0.242    2.45 0.016  0.129  
seqRun                 4      0.61   0.152    1.53 0.041  0.708  
Age                    1      0.40   0.398    4.02 0.027  0.345  
Parity                 1      0.18   0.176    1.78 0.012  0.894  
BMI                    1      0.35   0.351    3.54 0.024  0.932  
HLA_Time_Interaction   1      0.07   0.071    0.72 0.005  1.000  
Residuals            121     11.98   0.099         0.813  0.417  
Total                133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.3.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.47   0.236    2.39 0.032  0.344  
T1Dstatus              1      0.45   0.448    4.52 0.030  0.028 *
Days                   1      0.24   0.242    2.44 0.016  0.126  
seqRun                 4      0.61   0.152    1.53 0.041  0.687  
Age                    1      0.40   0.398    4.01 0.027  0.319  
Parity                 1      0.18   0.176    1.78 0.012  0.894  
BMI                    1      0.35   0.351    3.54 0.024  0.927  
HLA_Time_Interaction   1      0.06   0.062    0.63 0.004  0.775  
Residuals            121     11.99   0.099         0.813  0.165  
Total                133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.3.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days        1      0.27   0.266    2.69 0.018  0.076 . 
seqRun      4      0.60   0.150    1.52 0.041  0.701   
Age         1      0.39   0.389    3.94 0.026  0.616   
Parity      1      0.24   0.235    2.38 0.016  0.009 **
BMI         1      0.43   0.431    4.36 0.029  0.995   
T1Dstatus   1      0.37   0.374    3.79 0.025  0.068 . 
HLA         2      0.40   0.199    2.01 0.027  0.468   
Residuals 122     12.05   0.099         0.817  0.196   
Total     133     14.74                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.4 Parity

8.1.9.4.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                         Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                       2      0.47   0.236    2.40 0.032  0.357  
T1Dstatus                 1      0.45   0.448    4.54 0.030  0.031 *
Days                      1      0.24   0.242    2.46 0.016  0.117  
seqRun                    4      0.61   0.152    1.54 0.041  0.683  
Age                       1      0.40   0.398    4.03 0.027  0.336  
Parity                    1      0.18   0.176    1.78 0.012  0.912  
BMI                       1      0.35   0.351    3.55 0.024  0.931  
Parity_Time_Interaction   1      0.12   0.119    1.21 0.008  0.064 .
Residuals               121     11.93   0.099         0.809  0.132  
Total                   133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.4.2 Parity (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      0.47   0.236    2.39 0.032  0.353  
T1Dstatus   1      0.45   0.448    4.53 0.030  0.032 *
Days        1      0.24   0.242    2.45 0.016  0.139  
seqRun      4      0.61   0.152    1.53 0.041  0.690  
BMI         1      0.36   0.363    3.67 0.025  0.901  
Age         1      0.40   0.398    4.03 0.027  0.354  
Parity      1      0.16   0.163    1.65 0.011  0.930  
Residuals 122     12.05   0.099         0.817  0.191  
Total     133     14.74                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.4.3 Parity (no interaction but within T1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.266   0.133   1.239 0.106   0.26
T1Dstatus  1     0.079   0.079   0.735 0.031   0.74
seqRun     1     0.164   0.164   1.526 0.065   0.25
Age        1     0.137   0.137   1.276 0.054   0.81
BMI        1     0.158   0.158   1.467 0.063   0.32
Parity     1     0.106   0.106   0.988 0.042   0.45
Residuals 15     1.611   0.107         0.639   0.48
Total     22     2.521                 1.000       
8.1.9.4.4 Parity (no interaction but within T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.33  0.1648   1.690 0.070  0.316  
T1Dstatus  1      0.29  0.2885   2.957 0.062  0.044 *
seqRun     1      0.20  0.2032   2.084 0.043  0.911  
Age        1      0.21  0.2144   2.197 0.046  0.128  
BMI        1      0.16  0.1571   1.611 0.034  0.206  
Parity     1      0.07  0.0725   0.743 0.015  0.668  
Residuals 35      3.41  0.0975         0.730  0.103  
Total     42      4.68                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.4.5 Parity (no interaction but within T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.15  0.0748   0.709 0.021  0.857  
T1Dstatus  1      0.20  0.2020   1.915 0.028  0.065 .
seqRun     1      0.04  0.0374   0.355 0.005  0.104  
Age        1      0.15  0.1533   1.453 0.021  0.635  
BMI        1      0.23  0.2270   2.152 0.031  0.954  
Parity     1      0.19  0.1859   1.762 0.026  0.867  
Residuals 60      6.33  0.1055         0.869  0.722  
Total     67      7.29                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.5 Mode of delivery

8.1.9.5.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      0.47   0.236    2.44 0.032  0.366   
T1Dstatus              1      0.45   0.448    4.62 0.030  0.023 * 
MOD                    2      0.33   0.163    1.68 0.022  0.765   
Days                   1      0.24   0.245    2.53 0.017  0.121   
seqRun                 4      0.62   0.156    1.61 0.042  0.628   
Age                    1      0.54   0.541    5.58 0.037  0.002 **
Parity                 1      0.19   0.190    1.96 0.013  0.690   
BMI                    1      0.30   0.304    3.14 0.021  0.955   
MOD_Time_Interaction   1      0.07   0.067    0.70 0.005  0.997   
Residuals            119     11.53   0.097         0.782  0.287   
Total                133     14.74                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.5.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      0.47   0.236    2.44 0.032  0.354   
T1Dstatus              1      0.45   0.448    4.63 0.030  0.024 * 
MOD                    2      0.33   0.163    1.68 0.022  0.766   
Days                   1      0.24   0.245    2.53 0.017  0.106   
seqRun                 4      0.62   0.156    1.61 0.042  0.624   
Age                    1      0.54   0.541    5.59 0.037  0.003 **
Parity                 1      0.19   0.190    1.96 0.013  0.719   
BMI                    1      0.30   0.304    3.14 0.021  0.950   
MOD_Time_Interaction   1      0.08   0.083    0.86 0.006  1.000   
Residuals            119     11.51   0.097         0.781  0.424   
Total                133     14.74                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.5.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      0.47   0.236    2.44 0.032  0.309   
T1Dstatus              1      0.45   0.448    4.62 0.030  0.028 * 
MOD                    2      0.33   0.163    1.68 0.022  0.764   
Days                   1      0.24   0.245    2.52 0.017  0.122   
seqRun                 4      0.62   0.156    1.61 0.042  0.611   
Age                    1      0.54   0.541    5.58 0.037  0.004 **
Parity                 1      0.19   0.190    1.96 0.013  0.697   
BMI                    1      0.30   0.304    3.13 0.021  0.963   
MOD_Time_Interaction   1      0.06   0.055    0.57 0.004  1.000   
Residuals            119     11.54   0.097         0.783  0.475   
Total                133     14.74                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.5.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days        1      0.27   0.266    2.75 0.018  0.080 . 
seqRun      4      0.60   0.150    1.56 0.041  0.697   
Age         1      0.39   0.389    4.03 0.026  0.630   
Parity      1      0.24   0.235    2.43 0.016  0.007 **
BMI         1      0.43   0.431    4.46 0.029  0.988   
HLA         2      0.40   0.201    2.08 0.027  0.446   
T1Dstatus   1      0.37   0.369    3.82 0.025  0.056 . 
MOD         2      0.45   0.227    2.35 0.031  0.276   
Residuals 120     11.59   0.097         0.786  0.150   
Total     133     14.74                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.6 Carbohydrate intake

8.1.9.6.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.47   0.235    2.37 0.032   0.36  
T1Dstatus               1      0.43   0.434    4.36 0.030   0.04 *
Carbs                   1      0.19   0.190    1.91 0.013   0.53  
seqRun                  4      0.64   0.160    1.61 0.044   0.75  
Tri                     2      0.21   0.106    1.06 0.014   0.45  
Age                     1      0.42   0.416    4.19 0.028   0.29  
Parity                  1      0.17   0.174    1.74 0.012   0.86  
BMI                     1      0.37   0.374    3.76 0.026   0.74  
Carb_Time_Interaction   1      0.08   0.080    0.80 0.005   0.70  
Residuals             117     11.64   0.099         0.796   0.32  
Total                 131     14.63                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.6.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.47   0.235    2.36 0.032  0.318  
T1Dstatus               1      0.43   0.434    4.34 0.030  0.045 *
Carbs                   1      0.19   0.190    1.91 0.013  0.550  
seqRun                  4      0.64   0.160    1.61 0.044  0.730  
Tri                     2      0.21   0.106    1.06 0.014  0.428  
Age                     1      0.42   0.416    4.17 0.028  0.323  
Parity                  1      0.17   0.174    1.74 0.012  0.858  
BMI                     1      0.37   0.374    3.75 0.026  0.729  
Carb_Time_Interaction   1      0.04   0.041    0.41 0.003  0.992  
Residuals             117     11.68   0.100         0.798  0.377  
Total                 131     14.63                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.6.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.47   0.235    2.36 0.032  0.356  
T1Dstatus               1      0.43   0.434    4.35 0.030  0.045 *
Carbs                   1      0.19   0.190    1.91 0.013  0.526  
seqRun                  4      0.64   0.160    1.61 0.044  0.724  
Tri                     2      0.21   0.106    1.06 0.014  0.461  
Age                     1      0.42   0.416    4.18 0.028  0.325  
Parity                  1      0.17   0.174    1.74 0.012  0.866  
BMI                     1      0.37   0.374    3.75 0.026  0.734  
Carb_Time_Interaction   1      0.05   0.053    0.53 0.004  0.984  
Residuals             117     11.67   0.100         0.797  0.397  
Total                 131     14.63                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.6.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun      4      0.67   0.168    1.70 0.046  0.508  
Tri         2      0.23   0.113    1.13 0.015  0.455  
Age         1      0.41   0.413    4.16 0.028  0.522  
Parity      1      0.23   0.227    2.29 0.016  0.015 *
BMI         1      0.41   0.406    4.08 0.028  0.981  
HLA         2      0.40   0.201    2.03 0.027  0.457  
T1Dstatus   1      0.36   0.359    3.61 0.025  0.054 .
Carbs       1      0.21   0.206    2.07 0.014  0.392  
Residuals 118     11.72   0.099         0.801  0.265  
Total     131     14.63                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.7 Fibre intake

8.1.9.7.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.47   0.235    2.36 0.032  0.362  
T1Dstatus                1      0.43   0.434    4.35 0.030  0.029 *
Fiber                    1      0.16   0.157    1.58 0.011  0.684  
seqRun                   4      0.64   0.160    1.60 0.044  0.714  
Tri                      2      0.21   0.105    1.05 0.014  0.472  
Age                      1      0.45   0.449    4.51 0.031  0.117  
Parity                   1      0.18   0.177    1.78 0.012  0.832  
BMI                      1      0.35   0.349    3.50 0.024  0.837  
Fiber_Time_Interaction   1      0.08   0.084    0.84 0.006  0.209  
Residuals              117     11.66   0.100         0.797  0.283  
Total                  131     14.63                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.7.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.47   0.235    2.35 0.032  0.345  
T1Dstatus                1      0.43   0.434    4.33 0.030  0.043 *
Fiber                    1      0.16   0.157    1.57 0.011  0.694  
seqRun                   4      0.64   0.160    1.60 0.044  0.749  
Tri                      2      0.21   0.105    1.05 0.014  0.468  
Age                      1      0.45   0.449    4.49 0.031  0.120  
Parity                   1      0.18   0.177    1.77 0.012  0.822  
BMI                      1      0.35   0.349    3.49 0.024  0.836  
Fiber_Time_Interaction   1      0.03   0.026    0.26 0.002  0.993  
Residuals              117     11.72   0.100         0.801  0.407  
Total                  131     14.63                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.7.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.47   0.235    2.37 0.032  0.361  
T1Dstatus                1      0.43   0.434    4.36 0.030  0.038 *
Fiber                    1      0.16   0.157    1.58 0.011  0.714  
seqRun                   4      0.64   0.160    1.61 0.044  0.736  
Tri                      2      0.21   0.105    1.06 0.014  0.490  
Age                      1      0.45   0.449    4.51 0.031  0.124  
Parity                   1      0.18   0.177    1.78 0.012  0.838  
BMI                      1      0.35   0.349    3.51 0.024  0.819  
Fiber_Time_Interaction   1      0.10   0.102    1.02 0.007  0.901  
Residuals              117     11.64   0.100         0.796  0.408  
Total                  131     14.63                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.7.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun      4      0.67   0.168    1.69 0.046   0.53  
Tri         2      0.23   0.113    1.13 0.015   0.43  
Age         1      0.41   0.413    4.15 0.028   0.51  
Parity      1      0.23   0.227    2.29 0.016   0.02 *
BMI         1      0.41   0.406    4.08 0.028   0.99  
HLA         2      0.40   0.201    2.02 0.027   0.46  
T1Dstatus   1      0.36   0.359    3.61 0.025   0.07 .
Fiber       1      0.18   0.181    1.81 0.012   0.52  
Residuals 118     11.74   0.100         0.803   0.32  
Total     131     14.63                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

8.1.9.8 1,5-AG (glucose control measurement)

8.1.9.8.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.52   0.262    2.80 0.042  0.281  
T1Dstatus              1      0.52   0.522    5.56 0.042  0.018 *
Days                   1      0.14   0.143    1.53 0.012  0.478  
seqRun                 3      0.54   0.179    1.91 0.043  0.879  
Age                    1      0.44   0.438    4.67 0.035  0.043 *
Parity                 1      0.16   0.165    1.76 0.013  0.927  
BMI                    1      0.23   0.230    2.46 0.019  0.934  
AG15                   1      0.28   0.285    3.04 0.023  0.021 *
AG15_T1D_Interaction   1      0.17   0.172    1.83 0.014  0.145  
Residuals            100      9.37   0.094         0.757  0.029 *
Total                112     12.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.8.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.32   0.161    2.19 0.068  0.486  
Days       1      0.11   0.113    1.54 0.024  0.225  
seqRun     3      0.45   0.151    2.06 0.095  0.937  
Age        1      0.25   0.249    3.39 0.052  0.055 .
Parity     1      0.20   0.201    2.74 0.042  0.229  
BMI        1      0.41   0.411    5.60 0.087  0.124  
AG15       1      0.14   0.136    1.86 0.029  0.800  
Residuals 39      2.86   0.073         0.603  0.392  
Total     49      4.75                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
8.1.9.8.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.59   0.296    3.06 0.083  0.193  
Days       1      0.11   0.105    1.09 0.015  0.558  
seqRun     3      0.48   0.159    1.65 0.067  0.887  
Age        1      0.48   0.480    4.96 0.067  0.053 .
Parity     1      0.12   0.120    1.24 0.017  0.972  
BMI        1      0.08   0.076    0.79 0.011  1.000  
AG15       1      0.29   0.292    3.01 0.041  0.793  
Residuals 52      5.04   0.097         0.701  0.672  
Total     62      7.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9 Family taxonomic level

9.1 Microbial community composition analysis at Family level (Beta diversity analysis)

9.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
seqRun                 4      0.57   0.142    1.85 0.050  0.615   
Days                   1      0.18   0.184    2.40 0.016  0.131   
T1D_Time_Interaction   1      0.39   0.391    5.11 0.034  0.004 **
Age                    1      0.27   0.274    3.58 0.024  0.838   
Parity                 1      0.16   0.165    2.15 0.014  0.030 * 
BMI                    1      0.22   0.218    2.84 0.019  1.000   
HLA                    2      0.27   0.133    1.74 0.023  0.524   
T1Dstatus              1      0.06   0.065    0.85 0.006  0.895   
Residuals            121      9.26   0.077         0.813  0.578   
Total                133     11.39                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.004

9.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3     0.240  0.0800   0.901 0.118   0.58
Nulliparous     1     0.162  0.1622   1.827 0.080   0.11
Age_LMP         1     0.123  0.1234   1.389 0.061   0.20
BMI_conception  1     0.070  0.0703   0.792 0.035   0.59
HLA.6DRML       2     0.162  0.0808   0.909 0.080   0.55
T1Dstatus       1     0.117  0.1169   1.317 0.058   0.26
Residuals      13     1.154  0.0888         0.569       
Total          22     2.029                 1.000       
[1] 0.258

Beta diversity Plot

9.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun     3      0.55  0.1820   2.580 0.154  0.060 .
Age        1      0.12  0.1153   1.635 0.033  0.668  
Parity     1      0.11  0.1081   1.533 0.031  0.011 *
BMI        1      0.06  0.0623   0.883 0.018  0.687  
HLA        2      0.21  0.1056   1.498 0.060  0.271  
T1Dstatus  1      0.17  0.1658   2.351 0.047  0.096 .
Residuals 33      2.33  0.0705         0.658  0.130  
Total     42      3.54                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

9.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun     4      0.24  0.0612    0.75 0.043  0.634  
Age        1      0.09  0.0924    1.13 0.016  0.156  
Parity     1      0.14  0.1438    1.75 0.026  0.156  
BMI        1      0.28  0.2779    3.39 0.049  0.790  
HLA        2      0.05  0.0246    0.30 0.009  0.996  
T1Dstatus  1      0.15  0.1540    1.88 0.027  0.068 .
Residuals 57      4.68  0.0821         0.829  0.864  
Total     67      5.64                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

9.1.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.20   0.098    1.73 0.040  0.679  
seqRun     3      0.62   0.205    3.63 0.127  0.463  
Age        1      0.12   0.123    2.19 0.025  0.805  
Parity     1      0.13   0.129    2.29 0.027  0.131  
BMI        1      0.36   0.355    6.29 0.073  0.548  
Days       1      0.16   0.163    2.88 0.033  0.011 *
Residuals 58      3.27   0.056         0.674  0.242  
Total     67      4.86                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

9.1.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.20   0.098    1.72 0.040  0.682  
seqRun     3      0.62   0.205    3.60 0.127  0.460  
Age        1      0.12   0.123    2.17 0.025  0.817  
Parity     1      0.13   0.129    2.27 0.027  0.099 .
BMI        1      0.36   0.355    6.24 0.073  0.547  
Tri        2      0.19   0.096    1.69 0.040  0.020 *
Residuals 57      3.24   0.057         0.668         
Total     67      4.86                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

9.1.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.49   0.244    2.82 0.079  0.169  
seqRun     4      0.40   0.101    1.16 0.065  0.950  
Age        1      0.34   0.341    3.94 0.055  0.047 *
Parity     1      0.05   0.054    0.63 0.009  0.972  
BMI        1      0.05   0.048    0.55 0.008  1.000  
Days       1      0.08   0.083    0.96 0.013  0.425  
Residuals 55      4.76   0.087         0.771  0.455  
Total     65      6.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

9.1.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.49   0.244    2.80 0.079  0.184  
seqRun     4      0.40   0.101    1.15 0.065  0.947  
Age        1      0.34   0.341    3.90 0.055  0.048 *
Parity     1      0.05   0.054    0.62 0.009  0.983  
BMI        1      0.05   0.048    0.55 0.008  0.999  
Tri        2      0.13   0.066    0.76 0.021  0.745  
Residuals 54      4.71   0.087         0.763  0.641  
Total     65      6.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

9.1.9 Other factors

9.1.9.1 Age at conception

9.1.9.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.33   0.165    2.13 0.029  0.397  
T1Dstatus              1      0.34   0.340    4.40 0.030  0.051 .
seqRun                 4      0.60   0.149    1.93 0.052  0.562  
Tri                    2      0.16   0.081    1.04 0.014  0.565  
Age                    1      0.30   0.296    3.83 0.026  0.436  
Parity                 1      0.12   0.119    1.54 0.010  0.937  
BMI                    1      0.23   0.226    2.92 0.020  0.960  
Age_Time_Interaction   1      0.04   0.042    0.55 0.004  0.697  
Residuals            120      9.28   0.077         0.815  0.475  
Total                133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.33   0.165    2.13 0.029   0.43  
T1Dstatus              1      0.34   0.340    4.39 0.030   0.05 *
seqRun                 4      0.60   0.149    1.92 0.052   0.55  
Tri                    2      0.16   0.081    1.04 0.014   0.60  
Age                    1      0.30   0.296    3.83 0.026   0.46  
Parity                 1      0.12   0.119    1.54 0.010   0.94  
BMI                    1      0.23   0.226    2.91 0.020   0.96  
Age_Time_Interaction   1      0.02   0.023    0.30 0.002   0.88  
Residuals            120      9.30   0.078         0.816   0.48  
Total                133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.33   0.165    2.14 0.029  0.427  
T1Dstatus              1      0.34   0.340    4.40 0.030  0.048 *
seqRun                 4      0.60   0.149    1.93 0.052  0.544  
Tri                    2      0.16   0.081    1.04 0.014  0.592  
Age                    1      0.30   0.296    3.84 0.026  0.436  
Parity                 1      0.12   0.119    1.55 0.010  0.928  
BMI                    1      0.23   0.226    2.92 0.020  0.967  
Age_Time_Interaction   1      0.05   0.052    0.67 0.005  0.375  
Residuals            120      9.27   0.077         0.814  0.393  
Total                133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.1.4 Age at conception (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      0.33   0.165    2.14 0.029  0.390  
T1Dstatus   1      0.34   0.340    4.42 0.030  0.054 .
seqRun      4      0.60   0.149    1.93 0.052  0.547  
Tri         2      0.16   0.081    1.05 0.014  0.571  
Parity      1      0.12   0.121    1.57 0.011  0.925  
BMI         1      0.23   0.226    2.94 0.020  0.957  
Age         1      0.29   0.294    3.82 0.026  0.440  
Residuals 121      9.32   0.077         0.818  0.401  
Total     133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.2 Body max index (BMI)

9.1.9.2.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.33   0.165    2.13 0.029  0.426  
T1Dstatus              1      0.34   0.340    4.39 0.030  0.055 .
seqRun                 4      0.60   0.149    1.92 0.052  0.557  
Tri                    2      0.16   0.081    1.04 0.014  0.599  
Age                    1      0.30   0.296    3.82 0.026  0.440  
Parity                 1      0.12   0.119    1.54 0.010  0.943  
BMI                    1      0.23   0.226    2.91 0.020  0.959  
BMI_Time_Interaction   1      0.02   0.017    0.21 0.001  0.968  
Residuals            120      9.31   0.078         0.817  0.499  
Total                133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.2.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.33   0.165    2.13 0.029  0.406  
T1Dstatus              1      0.34   0.340    4.40 0.030  0.048 *
seqRun                 4      0.60   0.149    1.93 0.052  0.545  
Tri                    2      0.16   0.081    1.04 0.014  0.592  
Age                    1      0.30   0.296    3.83 0.026  0.438  
Parity                 1      0.12   0.119    1.54 0.010  0.922  
BMI                    1      0.23   0.226    2.92 0.020  0.967  
BMI_Time_Interaction   1      0.04   0.041    0.53 0.004  0.505  
Residuals            120      9.28   0.077         0.815  0.411  
Total                133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.2.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.33   0.165    2.14 0.029  0.430  
T1Dstatus              1      0.34   0.340    4.42 0.030  0.042 *
seqRun                 4      0.60   0.149    1.94 0.052  0.562  
Tri                    2      0.16   0.081    1.05 0.014  0.626  
Age                    1      0.30   0.296    3.85 0.026  0.450  
Parity                 1      0.12   0.119    1.55 0.010  0.914  
BMI                    1      0.23   0.226    2.93 0.020  0.963  
BMI_Time_Interaction   1      0.08   0.083    1.08 0.007  0.155  
Residuals            120      9.24   0.077         0.811  0.365  
Total                133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.2.4 BMI (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      0.33   0.165    2.14 0.029  0.432  
T1Dstatus   1      0.34   0.340    4.42 0.030  0.043 *
seqRun      4      0.60   0.149    1.93 0.052  0.536  
Tri         2      0.16   0.081    1.05 0.014  0.581  
Age         1      0.30   0.296    3.85 0.026  0.445  
Parity      1      0.12   0.119    1.55 0.010  0.935  
BMI         1      0.23   0.226    2.93 0.020  0.956  
Residuals 121      9.32   0.077         0.818  0.399  
Total     133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.3 HLA type

9.1.9.3.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.33   0.165    2.15 0.029  0.396  
T1Dstatus              1      0.34   0.340    4.43 0.030  0.054 .
Days                   1      0.22   0.222    2.90 0.020  0.070 .
seqRun                 4      0.55   0.138    1.80 0.048  0.648  
Age                    1      0.28   0.282    3.68 0.025  0.469  
Parity                 1      0.12   0.122    1.58 0.011  0.929  
BMI                    1      0.21   0.210    2.73 0.018  0.972  
HLA_Time_Interaction   1      0.05   0.046    0.60 0.004  0.996  
Residuals            121      9.29   0.077         0.815  0.359  
Total                133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.3.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.33   0.165    2.16 0.029  0.425  
T1Dstatus              1      0.34   0.340    4.44 0.030  0.051 .
Days                   1      0.22   0.222    2.90 0.020  0.064 .
seqRun                 4      0.55   0.138    1.80 0.048  0.630  
Age                    1      0.28   0.282    3.69 0.025  0.460  
Parity                 1      0.12   0.122    1.59 0.011  0.924  
BMI                    1      0.21   0.210    2.74 0.018  0.972  
HLA_Time_Interaction   1      0.07   0.069    0.89 0.006  0.997  
Residuals            121      9.27   0.077         0.813  0.462  
Total                133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.3.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.33   0.165    2.15 0.029  0.392  
T1Dstatus              1      0.34   0.340    4.43 0.030  0.048 *
Days                   1      0.22   0.222    2.90 0.020  0.064 .
seqRun                 4      0.55   0.138    1.79 0.048  0.596  
Age                    1      0.28   0.282    3.68 0.025  0.466  
Parity                 1      0.12   0.122    1.58 0.011  0.932  
BMI                    1      0.21   0.210    2.73 0.018  0.971  
HLA_Time_Interaction   1      0.04   0.041    0.53 0.004  0.277  
Residuals            121      9.29   0.077         0.816  0.231  
Total                133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.3.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days        1      0.24  0.2376    3.10 0.021  0.046 * 
seqRun      4      0.51  0.1283    1.68 0.045  0.840   
Age         1      0.28  0.2783    3.64 0.024  0.840   
Parity      1      0.18  0.1780    2.33 0.016  0.005 **
BMI         1      0.29  0.2901    3.79 0.025  0.981   
T1Dstatus   1      0.31  0.3095    4.04 0.027  0.052 . 
HLA         2      0.25  0.1254    1.64 0.022  0.616   
Residuals 122      9.33  0.0765         0.819  0.261   
Total     133     11.39                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.3.5 HLA (no interaction: T1)

Call:
adonis(formula = D ~ SeqRun + Nulliparous + BMI_conception +      T1Dstatus + Age_LMP + HLA.6DRML, data = Meta_df) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3     0.240  0.0800   0.901 0.118  0.588  
Nulliparous     1     0.162  0.1622   1.827 0.080  0.089 .
BMI_conception  1     0.088  0.0875   0.985 0.043  0.410  
T1Dstatus       1     0.180  0.1797   2.024 0.089  0.075 .
Age_LMP         1     0.071  0.0712   0.802 0.035  0.598  
HLA.6DRML       2     0.134  0.0668   0.753 0.066  0.694  
Residuals      13     1.154  0.0888         0.569         
Total          22     2.029                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.3.6 HLA type (no interaction: T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1      0.14  0.1431   2.035 0.040  0.596  
seqRun     3      0.53  0.1751   2.490 0.149  0.519  
Age        1      0.12  0.1224   1.741 0.035  0.703  
Parity     1      0.10  0.1020   1.451 0.029  0.786  
BMI        1      0.08  0.0815   1.159 0.023  0.901  
T1Dstatus  1      0.17  0.1723   2.451 0.049  0.058 .
HLA        2      0.14  0.0697   0.992 0.039  0.595  
Residuals 32      2.25  0.0703         0.636  0.300  
Total     42      3.54                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.3.7 HLA type (no interaction: T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1      0.20  0.1954    2.39 0.035  0.678  
seqRun     4      0.22  0.0553    0.67 0.039  0.528  
Age        1      0.08  0.0841    1.03 0.015  0.197  
Parity     1      0.16  0.1570    1.92 0.028  0.016 *
BMI        1      0.26  0.2617    3.20 0.046  0.914  
T1Dstatus  1      0.09  0.0921    1.12 0.016  0.333  
HLA        2      0.04  0.0222    0.27 0.008  0.997  
Residuals 56      4.58  0.0819         0.813  0.937  
Total     67      5.64                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.4 Parity

9.1.9.4.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                         Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                       2      0.33   0.165    2.17 0.029  0.429  
T1Dstatus                 1      0.34   0.340    4.47 0.030  0.051 .
Days                      1      0.22   0.222    2.92 0.020  0.082 .
seqRun                    4      0.55   0.138    1.81 0.048  0.629  
Age                       1      0.28   0.282    3.71 0.025  0.437  
Parity                    1      0.12   0.122    1.60 0.011  0.925  
BMI                       1      0.21   0.210    2.75 0.018  0.966  
Parity_Time_Interaction   1      0.12   0.120    1.58 0.011  0.051 .
Residuals               121      9.21   0.076         0.809  0.159  
Total                   133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.4.2 Parity (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      0.33   0.165    2.16 0.029  0.382  
T1Dstatus   1      0.34   0.340    4.45 0.030  0.058 .
Days        1      0.22   0.222    2.91 0.020  0.061 .
seqRun      4      0.55   0.138    1.80 0.048  0.634  
BMI         1      0.22   0.216    2.83 0.019  0.961  
Age         1      0.28   0.280    3.66 0.025  0.486  
Parity      1      0.12   0.118    1.54 0.010  0.970  
Residuals 122      9.33   0.077         0.819  0.253  
Total     133     11.39                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.4.3 Parity (no interaction but within T1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.222  0.1112   1.304 0.110   0.27
T1Dstatus  1     0.071  0.0706   0.828 0.035   0.63
seqRun     1     0.166  0.1662   1.950 0.082   0.26
Age        1     0.110  0.1100   1.291 0.054   0.78
BMI        1     0.066  0.0661   0.775 0.033   0.78
Parity     1     0.114  0.1143   1.340 0.056   0.49
Residuals 15     1.279  0.0853         0.630   0.52
Total     22     2.029                 1.000       
9.1.9.4.4 Parity (no interaction but within T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.21  0.1048   1.386 0.059  0.441  
T1Dstatus  1      0.22  0.2228   2.947 0.063  0.067 .
seqRun     1      0.16  0.1552   2.053 0.044  0.801  
Age        1      0.14  0.1408   1.863 0.040  0.161  
BMI        1      0.10  0.1010   1.336 0.029  0.235  
Parity     1      0.06  0.0612   0.809 0.017  0.732  
Residuals 35      2.65  0.0756         0.748  0.162  
Total     42      3.54                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.4.5 Parity (no interaction but within T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.09  0.0432   0.526 0.015  0.935  
T1Dstatus  1      0.18  0.1834   2.233 0.033  0.047 *
seqRun     1      0.03  0.0254   0.310 0.005  0.046 *
Age        1      0.11  0.1055   1.284 0.019  0.693  
BMI        1      0.16  0.1599   1.946 0.028  0.970  
Parity     1      0.15  0.1491   1.815 0.026  0.894  
Residuals 60      4.93  0.0822         0.874  0.782  
Total     67      5.64                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.5 Mode of delivery

9.1.9.5.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      0.33   0.165    2.20 0.029  0.412   
T1Dstatus              1      0.34   0.340    4.53 0.030  0.050 * 
MOD                    2      0.26   0.130    1.73 0.023  0.641   
Days                   1      0.23   0.226    3.01 0.020  0.055 . 
seqRun                 4      0.54   0.134    1.79 0.047  0.654   
Age                    1      0.42   0.417    5.56 0.037  0.007 **
Parity                 1      0.14   0.139    1.85 0.012  0.639   
BMI                    1      0.18   0.184    2.45 0.016  0.977   
MOD_Time_Interaction   1      0.03   0.029    0.39 0.003  1.000   
Residuals            119      8.93   0.075         0.784  0.341   
Total                133     11.39                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.5.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      0.33   0.165    2.21 0.029  0.412   
T1Dstatus              1      0.34   0.340    4.55 0.030  0.048 * 
MOD                    2      0.26   0.130    1.74 0.023  0.632   
Days                   1      0.23   0.226    3.02 0.020  0.052 . 
seqRun                 4      0.54   0.134    1.80 0.047  0.669   
Age                    1      0.42   0.417    5.58 0.037  0.009 **
Parity                 1      0.14   0.139    1.86 0.012  0.684   
BMI                    1      0.18   0.184    2.46 0.016  0.970   
MOD_Time_Interaction   1      0.06   0.059    0.78 0.005  1.000   
Residuals            119      8.90   0.075         0.781  0.432   
Total                133     11.39                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.5.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      0.33   0.165    2.20 0.029  0.422   
T1Dstatus              1      0.34   0.340    4.54 0.030  0.054 . 
MOD                    2      0.26   0.130    1.73 0.023  0.639   
Days                   1      0.23   0.226    3.01 0.020  0.055 . 
seqRun                 4      0.54   0.134    1.79 0.047  0.630   
Age                    1      0.42   0.417    5.56 0.037  0.002 **
Parity                 1      0.14   0.139    1.85 0.012  0.683   
BMI                    1      0.18   0.184    2.45 0.016  0.974   
MOD_Time_Interaction   1      0.03   0.030    0.41 0.003  1.000   
Residuals            119      8.93   0.075         0.784  0.525   
Total                133     11.39                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.5.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
Days        1      0.24  0.2376    3.18 0.021  0.053 . 
seqRun      4      0.51  0.1283    1.72 0.045  0.831   
Age         1      0.28  0.2783    3.73 0.024  0.851   
Parity      1      0.18  0.1780    2.38 0.016  0.005 **
BMI         1      0.29  0.2901    3.89 0.025  0.979   
HLA         2      0.27  0.1340    1.80 0.024  0.581   
T1Dstatus   1      0.29  0.2922    3.91 0.026  0.065 . 
MOD         2      0.38  0.1884    2.52 0.033  0.208   
Residuals 120      8.96  0.0747         0.786  0.192   
Total     133     11.39                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.6 Carbohydrate intake

9.1.9.6.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.33   0.164    2.13 0.029  0.428  
T1Dstatus               1      0.32   0.318    4.13 0.028  0.062 .
Carbs                   1      0.21   0.208    2.71 0.018  0.214  
seqRun                  4      0.58   0.146    1.90 0.052  0.626  
Tri                     2      0.17   0.087    1.13 0.015  0.445  
Age                     1      0.29   0.293    3.81 0.026  0.493  
Parity                  1      0.12   0.119    1.54 0.010  0.868  
BMI                     1      0.23   0.231    3.00 0.020  0.843  
Carb_Time_Interaction   1      0.05   0.055    0.71 0.005  0.826  
Residuals             117      9.00   0.077         0.796  0.371  
Total                 131     11.31                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.6.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.33   0.164    2.13 0.029  0.431  
T1Dstatus               1      0.32   0.318    4.13 0.028  0.063 .
Carbs                   1      0.21   0.208    2.70 0.018  0.202  
seqRun                  4      0.58   0.146    1.89 0.052  0.647  
Tri                     2      0.17   0.087    1.13 0.015  0.432  
Age                     1      0.29   0.293    3.80 0.026  0.503  
Parity                  1      0.12   0.119    1.54 0.010  0.867  
BMI                     1      0.23   0.231    2.99 0.020  0.852  
Carb_Time_Interaction   1      0.04   0.042    0.54 0.004  0.963  
Residuals             117      9.02   0.077         0.797  0.423  
Total                 131     11.31                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.6.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.33   0.164    2.13 0.029  0.445  
T1Dstatus               1      0.32   0.318    4.13 0.028  0.076 .
Carbs                   1      0.21   0.208    2.71 0.018  0.246  
seqRun                  4      0.58   0.146    1.89 0.052  0.628  
Tri                     2      0.17   0.087    1.13 0.015  0.438  
Age                     1      0.29   0.293    3.81 0.026  0.510  
Parity                  1      0.12   0.119    1.54 0.010  0.868  
BMI                     1      0.23   0.231    3.00 0.020  0.836  
Carb_Time_Interaction   1      0.05   0.047    0.62 0.004  0.921  
Residuals             117      9.01   0.077         0.796  0.441  
Total                 131     11.31                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.6.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
seqRun      4      0.58  0.1444    1.88 0.051  0.693   
Tri         2      0.17  0.0851    1.11 0.015  0.517   
Age         1      0.30  0.3020    3.93 0.027  0.703   
Parity      1      0.17  0.1664    2.17 0.015  0.008 **
BMI         1      0.27  0.2696    3.51 0.024  0.975   
HLA         2      0.27  0.1334    1.74 0.024  0.587   
T1Dstatus   1      0.28  0.2830    3.69 0.025  0.059 . 
Carbs       1      0.22  0.2187    2.85 0.019  0.162   
Residuals 118      9.06  0.0768         0.801  0.281   
Total     131     11.31                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.7 Fibre intake

9.1.9.7.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.33   0.164    2.11 0.029  0.456  
T1Dstatus                1      0.32   0.318    4.09 0.028  0.048 *
Fiber                    1      0.12   0.123    1.58 0.011  0.630  
seqRun                   4      0.59   0.146    1.88 0.052  0.589  
Tri                      2      0.17   0.086    1.11 0.015  0.422  
Age                      1      0.31   0.309    3.97 0.027  0.350  
Parity                   1      0.12   0.118    1.52 0.010  0.866  
BMI                      1      0.21   0.212    2.72 0.019  0.911  
Fiber_Time_Interaction   1      0.05   0.051    0.65 0.004  0.456  
Residuals              117      9.10   0.078         0.804  0.466  
Total                  131     11.31                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.7.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.33   0.164    2.10 0.029  0.411  
T1Dstatus                1      0.32   0.318    4.08 0.028  0.072 .
Fiber                    1      0.12   0.123    1.58 0.011  0.612  
seqRun                   4      0.59   0.146    1.88 0.052  0.616  
Tri                      2      0.17   0.086    1.11 0.015  0.445  
Age                      1      0.31   0.309    3.96 0.027  0.348  
Parity                   1      0.12   0.118    1.51 0.010  0.876  
BMI                      1      0.21   0.212    2.72 0.019  0.901  
Fiber_Time_Interaction   1      0.02   0.025    0.32 0.002  0.866  
Residuals              117      9.12   0.078         0.806  0.544  
Total                  131     11.31                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.7.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.33   0.164    2.12 0.029  0.457  
T1Dstatus                1      0.32   0.318    4.11 0.028  0.066 .
Fiber                    1      0.12   0.123    1.59 0.011  0.576  
seqRun                   4      0.59   0.146    1.89 0.052  0.631  
Tri                      2      0.17   0.086    1.11 0.015  0.433  
Age                      1      0.31   0.309    3.99 0.027  0.333  
Parity                   1      0.12   0.118    1.52 0.010  0.883  
BMI                      1      0.21   0.212    2.74 0.019  0.907  
Fiber_Time_Interaction   1      0.09   0.086    1.11 0.008  0.512  
Residuals              117      9.06   0.077         0.801  0.489  
Total                  131     11.31                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.7.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun      4      0.58  0.1444    1.86 0.051  0.633  
Tri         2      0.17  0.0851    1.10 0.015  0.504  
Age         1      0.30  0.3020    3.90 0.027  0.701  
Parity      1      0.17  0.1664    2.15 0.015  0.021 *
BMI         1      0.27  0.2696    3.48 0.024  0.978  
HLA         2      0.27  0.1334    1.72 0.024  0.543  
T1Dstatus   1      0.28  0.2830    3.65 0.025  0.065 .
Fiber       1      0.13  0.1297    1.67 0.011  0.482  
Residuals 118      9.15  0.0775         0.809  0.457  
Total     131     11.31                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

9.1.9.8 1,5-AG (glucose control measurement)

9.1.9.8.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      0.33   0.164    2.20 0.034  0.457   
T1Dstatus              1      0.44   0.441    5.92 0.045  0.018 * 
Days                   1      0.13   0.129    1.73 0.013  0.297   
seqRun                 3      0.46   0.152    2.04 0.047  0.915   
Age                    1      0.33   0.330    4.44 0.034  0.073 . 
Parity                 1      0.12   0.118    1.58 0.012  0.941   
BMI                    1      0.13   0.128    1.72 0.013  0.986   
AG15                   1      0.22   0.223    2.99 0.023  0.007 **
AG15_T1D_Interaction   1      0.13   0.133    1.78 0.014  0.621   
Residuals            100      7.45   0.074         0.765  0.075 . 
Total                112      9.73                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.8.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2      0.19  0.0944    1.70 0.053  0.680  
Days       1      0.11  0.1075    1.93 0.030  0.165  
seqRun     3      0.44  0.1478    2.66 0.125  0.825  
Age        1      0.16  0.1570    2.83 0.044  0.069 .
Parity     1      0.13  0.1310    2.36 0.037  0.137  
BMI        1      0.23  0.2272    4.09 0.064  0.182  
AG15       1      0.13  0.1324    2.38 0.037  0.647  
Residuals 39      2.17  0.0555         0.610  0.392  
Total     49      3.55                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
9.1.9.8.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2      0.43  0.2141    2.63 0.074   0.26
Days       1      0.09  0.0889    1.09 0.015   0.44
seqRun     3      0.36  0.1213    1.49 0.063   0.87
Age        1      0.31  0.3140    3.86 0.055   0.19
Parity     1      0.07  0.0652    0.80 0.011   0.98
BMI        1      0.05  0.0502    0.62 0.009   1.00
AG15       1      0.22  0.2166    2.66 0.038   0.75
Residuals 52      4.23  0.0814         0.735   0.78
Total     62      5.76                 1.000       

10 Order taxonomic level

10.1 Microbial community composition analysis at Order level (Beta diversity analysis)

10.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun                 4      0.21  0.0535    1.65 0.045  0.519  
Days                   1      0.04  0.0362    1.12 0.008  0.599  
T1D_Time_Interaction   1      0.28  0.2766    8.53 0.058  0.039 *
Age                    1      0.06  0.0619    1.91 0.013  0.637  
Parity                 1      0.08  0.0798    2.46 0.017  0.487  
BMI                    1      0.07  0.0700    2.16 0.015  0.767  
HLA                    2      0.07  0.0348    1.07 0.015  0.673  
T1Dstatus              1      0.02  0.0240    0.74 0.005  0.675  
Residuals            121      3.92  0.0324         0.825  0.671  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.039

10.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3     0.107  0.0356    1.07 0.120  0.381  
Nulliparous     1     0.200  0.1999    6.00 0.225  0.011 *
Age_LMP         1     0.022  0.0220    0.66 0.025  0.514  
BMI_conception  1     0.009  0.0088    0.26 0.010  0.843  
HLA.6DRML       2     0.049  0.0244    0.73 0.055  0.566  
T1Dstatus       1     0.068  0.0681    2.04 0.077  0.133  
Residuals      13     0.433  0.0333         0.488         
Total          22     0.888                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.133

Beta diversity Plot

10.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3     0.303  0.1010   2.699 0.171  0.001 ***
Age        1     0.028  0.0283   0.757 0.016  0.484    
Parity     1     0.029  0.0288   0.769 0.016  0.173    
BMI        1     0.039  0.0390   1.043 0.022  0.359    
HLA        2     0.040  0.0202   0.539 0.023  0.748    
T1Dstatus  1     0.096  0.0959   2.564 0.054  0.123    
Residuals 33     1.235  0.0374         0.698  0.384    
Total     42     1.770                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

10.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun     4     0.093  0.0234    0.84 0.046  0.796  
Age        1     0.019  0.0187    0.67 0.009  0.821  
Parity     1     0.122  0.1217    4.37 0.060  0.822  
BMI        1     0.113  0.1130    4.06 0.055  0.461  
HLA        2     0.035  0.0176    0.63 0.017  0.635  
T1Dstatus  1     0.075  0.0748    2.69 0.037  0.077 .
Residuals 57     1.587  0.0278         0.776  0.292  
Total     67     2.044                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

10.1.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.062  0.0309    1.64 0.038       
seqRun     3     0.194  0.0647    3.44 0.121       
Age        1     0.025  0.0253    1.34 0.016       
Parity     1     0.104  0.1036    5.50 0.064       
BMI        1     0.072  0.0722    3.84 0.045       
Days       1     0.060  0.0596    3.17 0.037       
Residuals 58     1.091  0.0188         0.679       
Total     67     1.608                 1.000       

Beta diversity Plot

10.1.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.062  0.0309    1.64 0.038   0.54
seqRun     3     0.194  0.0647    3.43 0.121   0.68
Age        1     0.025  0.0253    1.34 0.016   0.78
Parity     1     0.104  0.1036    5.50 0.064   0.14
BMI        1     0.072  0.0722    3.83 0.045   0.43
Tri        2     0.077  0.0384    2.04 0.048   0.14
Residuals 57     1.074  0.0188         0.668   0.27
Total     67     1.608                 1.000       

Beta diversity Plot

10.1.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.214  0.1069    2.55 0.074  0.289  
seqRun     4     0.119  0.0297    0.71 0.041  0.865  
Age        1     0.196  0.1964    4.68 0.068  0.025 *
Parity     1     0.032  0.0316    0.75 0.011  0.780  
BMI        1     0.007  0.0069    0.16 0.002  0.993  
Days       1     0.016  0.0157    0.38 0.005  0.712  
Residuals 55     2.305  0.0419         0.798  0.319  
Total     65     2.888                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

10.1.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.214  0.1069    2.56 0.074  0.277  
seqRun     4     0.119  0.0297    0.71 0.041  0.885  
Age        1     0.196  0.1964    4.71 0.068  0.026 *
Parity     1     0.032  0.0316    0.76 0.011  0.804  
BMI        1     0.007  0.0069    0.17 0.002  0.994  
Tri        2     0.069  0.0346    0.83 0.024  0.808  
Residuals 54     2.252  0.0417         0.780  0.434  
Total     65     2.888                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

10.1.9 Other factors

10.1.9.1 Age at conception

10.1.9.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.57 0.021  0.540  
T1Dstatus              1      0.22  0.2230    6.89 0.047  0.043 *
seqRun                 4      0.24  0.0606    1.87 0.051  0.183  
Tri                    2      0.08  0.0376    1.16 0.016  0.794  
Age                    1      0.07  0.0706    2.18 0.015  0.465  
Parity                 1      0.07  0.0733    2.26 0.015  0.786  
BMI                    1      0.06  0.0595    1.84 0.013  0.945  
Age_Time_Interaction   1      0.03  0.0272    0.84 0.006  0.299  
Residuals            120      3.88  0.0324         0.816  0.340  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.56 0.021  0.540  
T1Dstatus              1      0.22  0.2230    6.85 0.047  0.055 .
seqRun                 4      0.24  0.0606    1.86 0.051  0.186  
Tri                    2      0.08  0.0376    1.16 0.016  0.790  
Age                    1      0.07  0.0706    2.17 0.015  0.459  
Parity                 1      0.07  0.0733    2.25 0.015  0.797  
BMI                    1      0.06  0.0595    1.83 0.013  0.962  
Age_Time_Interaction   1      0.00  0.0049    0.15 0.001  0.830  
Residuals            120      3.90  0.0325         0.821  0.399  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.57 0.021  0.548  
T1Dstatus              1      0.22  0.2230    6.90 0.047  0.053 .
seqRun                 4      0.24  0.0606    1.87 0.051  0.188  
Tri                    2      0.08  0.0376    1.16 0.016  0.801  
Age                    1      0.07  0.0706    2.19 0.015  0.493  
Parity                 1      0.07  0.0733    2.27 0.015  0.784  
BMI                    1      0.06  0.0595    1.84 0.013  0.945  
Age_Time_Interaction   1      0.03  0.0325    1.01 0.007  0.136  
Residuals            120      3.88  0.0323         0.815  0.308  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.1.4 Age at conception (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      0.10  0.0509    1.57 0.021  0.526  
T1Dstatus   1      0.22  0.2230    6.90 0.047  0.051 .
seqRun      4      0.24  0.0606    1.87 0.051  0.211  
Tri         2      0.08  0.0376    1.16 0.016  0.799  
Parity      1      0.07  0.0737    2.28 0.016  0.830  
BMI         1      0.06  0.0557    1.72 0.012  0.961  
Age         1      0.07  0.0740    2.29 0.016  0.509  
Residuals 121      3.91  0.0323         0.822  0.360  
Total     133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.2 Body max index (BMI)

10.1.9.2.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.57 0.021  0.547  
T1Dstatus              1      0.22  0.2230    6.86 0.047  0.059 .
seqRun                 4      0.24  0.0606    1.86 0.051  0.208  
Tri                    2      0.08  0.0376    1.16 0.016  0.801  
Age                    1      0.07  0.0706    2.17 0.015  0.471  
Parity                 1      0.07  0.0733    2.26 0.015  0.783  
BMI                    1      0.06  0.0595    1.83 0.013  0.952  
BMI_Time_Interaction   1      0.01  0.0114    0.35 0.002  0.699  
Residuals            120      3.90  0.0325         0.820  0.438  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.2.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model     R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.56  0.021  0.523  
T1Dstatus              1      0.22  0.2230    6.84  0.047  0.055 .
seqRun                 4      0.24  0.0606    1.86  0.051  0.197  
Tri                    2      0.08  0.0376    1.15  0.016  0.822  
Age                    1      0.07  0.0706    2.17  0.015  0.491  
Parity                 1      0.07  0.0733    2.25  0.015  0.783  
BMI                    1      0.06  0.0595    1.83  0.013  0.939  
BMI_Time_Interaction   1      0.00 -0.0034   -0.10 -0.001  0.959  
Residuals            120      3.91  0.0326          0.823  0.417  
Total                133      4.76                  1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.2.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.57 0.021  0.552  
T1Dstatus              1      0.22  0.2230    6.86 0.047  0.048 *
seqRun                 4      0.24  0.0606    1.86 0.051  0.179  
Tri                    2      0.08  0.0376    1.16 0.016  0.807  
Age                    1      0.07  0.0706    2.17 0.015  0.473  
Parity                 1      0.07  0.0733    2.25 0.015  0.804  
BMI                    1      0.06  0.0595    1.83 0.013  0.954  
BMI_Time_Interaction   1      0.01  0.0092    0.28 0.002  0.613  
Residuals            120      3.90  0.0325         0.820  0.376  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.2.4 BMI (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      0.10  0.0509    1.57 0.021  0.541  
T1Dstatus   1      0.22  0.2230    6.90 0.047  0.044 *
seqRun      4      0.24  0.0606    1.87 0.051  0.176  
Tri         2      0.08  0.0376    1.16 0.016  0.782  
Age         1      0.07  0.0706    2.19 0.015  0.477  
Parity      1      0.07  0.0733    2.27 0.015  0.768  
BMI         1      0.06  0.0595    1.84 0.013  0.949  
Residuals 121      3.91  0.0323         0.822  0.357  
Total     133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.3 HLA type

10.1.9.3.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.56 0.021  0.522  
T1Dstatus              1      0.22  0.2230    6.86 0.047  0.052 .
Days                   1      0.01  0.0111    0.34 0.002  0.889  
seqRun                 4      0.26  0.0653    2.01 0.055  0.244  
Age                    1      0.07  0.0684    2.10 0.014  0.425  
Parity                 1      0.08  0.0758    2.33 0.016  0.778  
BMI                    1      0.06  0.0564    1.73 0.012  0.943  
HLA_Time_Interaction   1      0.02  0.0219    0.67 0.005  0.678  
Residuals            121      3.94  0.0325         0.828  0.270  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.3.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.56 0.021   0.55  
T1Dstatus              1      0.22  0.2230    6.85 0.047   0.04 *
Days                   1      0.01  0.0111    0.34 0.002   0.89  
seqRun                 4      0.26  0.0653    2.00 0.055   0.27  
Age                    1      0.07  0.0684    2.10 0.014   0.46  
Parity                 1      0.08  0.0758    2.33 0.016   0.74  
BMI                    1      0.06  0.0564    1.73 0.012   0.95  
HLA_Time_Interaction   1      0.02  0.0176    0.54 0.004   1.00  
Residuals            121      3.94  0.0326         0.829   0.54  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.3.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.56 0.021  0.539  
T1Dstatus              1      0.22  0.2230    6.82 0.047  0.045 *
Days                   1      0.01  0.0111    0.34 0.002  0.909  
seqRun                 4      0.26  0.0653    2.00 0.055  0.237  
Age                    1      0.07  0.0684    2.09 0.014  0.430  
Parity                 1      0.08  0.0758    2.32 0.016  0.764  
BMI                    1      0.06  0.0564    1.72 0.012  0.950  
HLA_Time_Interaction   1      0.00  0.0026    0.08 0.001  0.939  
Residuals            121      3.96  0.0327         0.832  0.289  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.3.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days        1      0.02  0.0167    0.52 0.004   0.76  
seqRun      4      0.23  0.0584    1.80 0.049   0.65  
Age         1      0.06  0.0646    1.99 0.014   0.64  
Parity      1      0.09  0.0927    2.86 0.020   0.33  
BMI         1      0.11  0.1073    3.31 0.023   0.31  
T1Dstatus   1      0.21  0.2119    6.53 0.045   0.05 *
HLA         2      0.07  0.0354    1.09 0.015   0.69  
Residuals 122      3.96  0.0324         0.832   0.28  
Total     133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.4 Parity

10.1.9.4.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                         Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                       2      0.10  0.0509    1.61 0.021  0.538  
T1Dstatus                 1      0.22  0.2230    7.05 0.047  0.042 *
Days                      1      0.01  0.0111    0.35 0.002  0.895  
seqRun                    4      0.26  0.0653    2.06 0.055  0.260  
Age                       1      0.07  0.0684    2.16 0.014  0.422  
Parity                    1      0.08  0.0758    2.40 0.016  0.766  
BMI                       1      0.06  0.0564    1.78 0.012  0.929  
Parity_Time_Interaction   1      0.13  0.1305    4.12 0.027  0.043 *
Residuals               121      3.83  0.0316         0.805  0.122  
Total                   133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.4.2 Parity (no interaction but within T1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.053  0.0263    0.69 0.059  0.633  
T1Dstatus  1     0.011  0.0107    0.28 0.012  0.860  
seqRun     1     0.074  0.0744    1.95 0.084  0.045 *
Age        1     0.036  0.0359    0.94 0.040  0.721  
BMI        1     0.016  0.0160    0.42 0.018  0.751  
Parity     1     0.126  0.1261    3.31 0.142  0.405  
Residuals 15     0.572  0.0381         0.644  0.736  
Total     22     0.888                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.4.3 Parity (no interaction but within T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.051  0.0253    0.63 0.029  0.725  
T1Dstatus  1     0.173  0.1729    4.34 0.098  0.056 .
seqRun     1     0.078  0.0784    1.97 0.044  0.914  
Age        1     0.032  0.0318    0.80 0.018  0.251  
BMI        1     0.015  0.0151    0.38 0.009  0.478  
Parity     1     0.026  0.0255    0.64 0.014  0.868  
Residuals 35     1.396  0.0399         0.788  0.491  
Total     42     1.770                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.4.4 Parity (no interaction but within T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.045  0.0223    0.79 0.022   0.59  
T1Dstatus  1     0.106  0.1057    3.73 0.052   0.06 .
seqRun     1     0.005  0.0052    0.18 0.003   0.06 .
Age        1     0.016  0.0161    0.57 0.008   0.76  
BMI        1     0.024  0.0241    0.85 0.012   0.88  
Parity     1     0.146  0.1464    5.16 0.072   0.79  
Residuals 60     1.701  0.0284         0.833   0.30  
Total     67     2.044                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.5 Mode of delivery

10.1.9.5.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.56 0.021  0.540  
T1Dstatus              1      0.22  0.2230    6.84 0.047  0.054 .
MOD                    2      0.08  0.0412    1.26 0.017  0.630  
Days                   1      0.01  0.0105    0.32 0.002  0.890  
seqRun                 4      0.22  0.0556    1.70 0.047  0.470  
Age                    1      0.09  0.0890    2.73 0.019  0.214  
Parity                 1      0.08  0.0786    2.41 0.017  0.599  
BMI                    1      0.05  0.0455    1.39 0.010  0.948  
MOD_Time_Interaction   1      0.02  0.0209    0.64 0.004  0.982  
Residuals            119      3.88  0.0326         0.816  0.669  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.5.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.57 0.021  0.555  
T1Dstatus              1      0.22  0.2230    6.87 0.047  0.039 *
MOD                    2      0.08  0.0412    1.27 0.017  0.624  
Days                   1      0.01  0.0105    0.32 0.002  0.898  
seqRun                 4      0.22  0.0556    1.71 0.047  0.485  
Age                    1      0.09  0.0890    2.74 0.019  0.204  
Parity                 1      0.08  0.0786    2.42 0.017  0.610  
BMI                    1      0.05  0.0455    1.40 0.010  0.945  
MOD_Time_Interaction   1      0.04  0.0416    1.28 0.009  0.040 *
Residuals            119      3.86  0.0324         0.812  0.407  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.5.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.10  0.0509    1.56 0.021  0.563  
T1Dstatus              1      0.22  0.2230    6.84 0.047  0.042 *
MOD                    2      0.08  0.0412    1.26 0.017  0.651  
Days                   1      0.01  0.0105    0.32 0.002  0.902  
seqRun                 4      0.22  0.0556    1.71 0.047  0.480  
Age                    1      0.09  0.0890    2.73 0.019  0.203  
Parity                 1      0.08  0.0786    2.41 0.017  0.624  
BMI                    1      0.05  0.0455    1.40 0.010  0.934  
MOD_Time_Interaction   1      0.02  0.0241    0.74 0.005  0.994  
Residuals            119      3.88  0.0326         0.816  0.700  
Total                133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.5.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days        1      0.02  0.0167    0.51 0.004  0.780  
seqRun      4      0.23  0.0584    1.80 0.049  0.637  
Age         1      0.06  0.0646    1.99 0.014  0.638  
Parity      1      0.09  0.0927    2.85 0.020  0.295  
BMI         1      0.11  0.1073    3.30 0.023  0.323  
HLA         2      0.11  0.0528    1.62 0.022  0.496  
T1Dstatus   1      0.18  0.1770    5.44 0.037  0.074 .
MOD         2      0.06  0.0277    0.85 0.012  0.793  
Residuals 120      3.90  0.0325         0.821  0.485  
Total     133      4.76                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.5.5 Mode of delivery (no interaction: T1)

Call:
adonis(formula = D ~ SeqRun + Nulliparous + BMI_conception +      T1Dstatus + Age_LMP + HLA.6DRML + MOD, data = Meta_df) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
SeqRun          3     0.107  0.0356    1.09 0.120  0.376   
Nulliparous     1     0.200  0.1999    6.10 0.225  0.009 **
BMI_conception  1     0.011  0.0114    0.35 0.013  0.794   
T1Dstatus       1     0.093  0.0929    2.83 0.105  0.069 . 
Age_LMP         1     0.017  0.0165    0.50 0.019  0.631   
HLA.6DRML       2     0.027  0.0133    0.41 0.030  0.848   
MOD             2     0.072  0.0362    1.11 0.082  0.371   
Residuals      11     0.361  0.0328         0.406          
Total          22     0.888                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.5.6 Mode of delivery (no interaction: T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1     0.057  0.0572   1.491 0.032  0.775  
seqRun     3     0.279  0.0930   2.422 0.158  0.184  
Age        1     0.031  0.0306   0.798 0.017  0.675  
Parity     1     0.027  0.0273   0.710 0.015  0.215  
BMI        1     0.065  0.0646   1.682 0.036  0.802  
HLA        2     0.019  0.0096   0.250 0.011  0.951  
T1Dstatus  1     0.114  0.1142   2.974 0.064  0.065 .
MOD        2     0.026  0.0132   0.344 0.015  0.912  
Residuals 30     1.152  0.0384         0.651  0.743  
Total     42     1.770                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.5.7 Mode of delivery (no interaction: T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
Days       1     0.098  0.0985    3.51 0.048  0.001 ***
seqRun     4     0.081  0.0204    0.73 0.040  0.480    
Age        1     0.015  0.0154    0.55 0.008  0.827    
Parity     1     0.137  0.1365    4.87 0.067  0.235    
BMI        1     0.105  0.1045    3.73 0.051  0.466    
HLA        2     0.024  0.0122    0.43 0.012  0.795    
T1Dstatus  1     0.037  0.0369    1.32 0.018  0.239    
MOD        2     0.033  0.0166    0.59 0.016  0.663    
Residuals 54     1.513  0.0280         0.740  0.667    
Total     67     2.044                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.6 Carbohydrate intake

10.1.9.6.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.10  0.0494    1.52 0.021  0.565  
T1Dstatus               1      0.21  0.2101    6.47 0.044  0.056 .
Carbs                   1      0.03  0.0278    0.86 0.006  0.678  
seqRun                  4      0.26  0.0660    2.03 0.056  0.193  
Tri                     2      0.08  0.0389    1.20 0.016  0.705  
Age                     1      0.10  0.1022    3.15 0.022  0.152  
Parity                  1      0.06  0.0645    1.99 0.014  0.716  
BMI                     1      0.06  0.0595    1.83 0.013  0.879  
Carb_Time_Interaction   1      0.03  0.0271    0.83 0.006  0.800  
Residuals             117      3.80  0.0325         0.803  0.475  
Total                 131      4.73                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.6.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.10  0.0494    1.52 0.021  0.576  
T1Dstatus               1      0.21  0.2101    6.45 0.044  0.055 .
Carbs                   1      0.03  0.0278    0.85 0.006  0.679  
seqRun                  4      0.26  0.0660    2.03 0.056  0.172  
Tri                     2      0.08  0.0389    1.20 0.016  0.726  
Age                     1      0.10  0.1022    3.14 0.022  0.153  
Parity                  1      0.06  0.0645    1.98 0.014  0.761  
BMI                     1      0.06  0.0595    1.83 0.013  0.874  
Carb_Time_Interaction   1      0.02  0.0159    0.49 0.003  0.874  
Residuals             117      3.81  0.0326         0.805  0.458  
Total                 131      4.73                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.6.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.10  0.0494    1.52 0.021  0.585  
T1Dstatus               1      0.21  0.2101    6.45 0.044  0.066 .
Carbs                   1      0.03  0.0278    0.85 0.006  0.679  
seqRun                  4      0.26  0.0660    2.03 0.056  0.185  
Tri                     2      0.08  0.0389    1.19 0.016  0.724  
Age                     1      0.10  0.1022    3.14 0.022  0.153  
Parity                  1      0.06  0.0645    1.98 0.014  0.751  
BMI                     1      0.06  0.0595    1.83 0.013  0.872  
Carb_Time_Interaction   1      0.01  0.0128    0.39 0.003  0.824  
Residuals             117      3.81  0.0326         0.806  0.434  
Total                 131      4.73                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.6.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun      4      0.23  0.0582    1.80 0.049   0.53  
Tri         2      0.09  0.0441    1.36 0.019   0.71  
Age         1      0.07  0.0719    2.22 0.015   0.69  
Parity      1      0.08  0.0798    2.46 0.017   0.37  
BMI         1      0.10  0.0957    2.95 0.020   0.64  
HLA         2      0.09  0.0470    1.45 0.020   0.54  
T1Dstatus   1      0.17  0.1653    5.10 0.035   0.06 .
Carbs       1      0.08  0.0771    2.38 0.016   0.26  
Residuals 118      3.82  0.0324         0.809   0.36  
Total     131      4.73                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.7 Fibre intake

10.1.9.7.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.10  0.0494    1.50 0.021  0.555  
T1Dstatus                1      0.21  0.2101    6.36 0.044  0.057 .
Fiber                    1      0.01  0.0070    0.21 0.001  0.965  
seqRun                   4      0.25  0.0625    1.89 0.053  0.279  
Tri                      2      0.07  0.0371    1.12 0.016  0.733  
Age                      1      0.09  0.0897    2.72 0.019  0.259  
Parity                   1      0.07  0.0680    2.06 0.014  0.677  
BMI                      1      0.05  0.0531    1.61 0.011  0.916  
Fiber_Time_Interaction   1      0.02  0.0151    0.46 0.003  0.577  
Residuals              117      3.86  0.0330         0.817  0.530  
Total                  131      4.73                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.7.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.10  0.0494    1.49 0.021  0.578  
T1Dstatus                1      0.21  0.2101    6.34 0.044  0.057 .
Fiber                    1      0.01  0.0070    0.21 0.001  0.980  
seqRun                   4      0.25  0.0625    1.89 0.053  0.241  
Tri                      2      0.07  0.0371    1.12 0.016  0.755  
Age                      1      0.09  0.0897    2.71 0.019  0.251  
Parity                   1      0.07  0.0680    2.05 0.014  0.680  
BMI                      1      0.05  0.0531    1.60 0.011  0.901  
Fiber_Time_Interaction   1      0.00  0.0027    0.08 0.001  0.919  
Residuals              117      3.88  0.0331         0.820  0.576  
Total                  131      4.73                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.7.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.10  0.0494    1.49 0.021  0.593  
T1Dstatus                1      0.21  0.2101    6.36 0.044  0.069 .
Fiber                    1      0.01  0.0070    0.21 0.001  0.973  
seqRun                   4      0.25  0.0625    1.89 0.053  0.266  
Tri                      2      0.07  0.0371    1.12 0.016  0.740  
Age                      1      0.09  0.0897    2.72 0.019  0.261  
Parity                   1      0.07  0.0680    2.06 0.014  0.677  
BMI                      1      0.05  0.0531    1.61 0.011  0.898  
Fiber_Time_Interaction   1      0.01  0.0139    0.42 0.003  0.511  
Residuals              117      3.86  0.0330         0.817  0.573  
Total                  131      4.73                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.7.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun      4      0.23  0.0582    1.77 0.049  0.536  
Tri         2      0.09  0.0441    1.34 0.019  0.720  
Age         1      0.07  0.0719    2.19 0.015  0.681  
Parity      1      0.08  0.0798    2.43 0.017  0.342  
BMI         1      0.10  0.0957    2.91 0.020  0.606  
HLA         2      0.09  0.0470    1.43 0.020  0.557  
T1Dstatus   1      0.17  0.1653    5.03 0.035  0.078 .
Fiber       1      0.02  0.0230    0.70 0.005  0.723  
Residuals 118      3.88  0.0329         0.820  0.504  
Total     131      4.73                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

10.1.9.8 1,5-AG (glucose control measurement)

10.1.9.8.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.12  0.0622    1.96 0.031  0.469  
T1Dstatus              1      0.26  0.2645    8.35 0.066  0.030 *
Days                   1      0.01  0.0116    0.37 0.003  0.898  
seqRun                 3      0.17  0.0564    1.78 0.042  0.686  
Age                    1      0.09  0.0948    2.99 0.024  0.118  
Parity                 1      0.05  0.0492    1.55 0.012  0.812  
BMI                    1      0.02  0.0228    0.72 0.006  0.970  
AG15                   1      0.08  0.0835    2.64 0.021  0.028 *
AG15_T1D_Interaction   1      0.05  0.0459    1.45 0.011  0.717  
Residuals            100      3.17  0.0317         0.785  0.168  
Total                112      4.03                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.8.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.022  0.0112    0.61 0.020  0.957  
Days       1     0.054  0.0537    2.92 0.048  0.047 *
seqRun     3     0.150  0.0502    2.73 0.135  0.296  
Age        1     0.022  0.0221    1.20 0.020  0.352  
Parity     1     0.064  0.0641    3.48 0.058  0.570  
BMI        1     0.031  0.0305    1.66 0.027  0.285  
AG15       1     0.050  0.0500    2.72 0.045  0.021 *
Residuals 39     0.718  0.0184         0.646  0.220  
Total     49     1.111                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
10.1.9.8.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.173  0.0866    2.18 0.066  0.411  
Days       1     0.013  0.0131    0.33 0.005  0.806  
seqRun     3     0.100  0.0333    0.84 0.038  0.907  
Age        1     0.150  0.1501    3.78 0.057  0.067 .
Parity     1     0.025  0.0254    0.64 0.010  0.902  
BMI        1     0.012  0.0123    0.31 0.005  0.974  
AG15       1     0.084  0.0838    2.11 0.032  0.806  
Residuals 52     2.067  0.0397         0.787  0.799  
Total     62     2.625                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

11 Phylum taxonomic level

11.1 Microbial community composition analysis at Phylum level (Beta diversity analysis)

11.1.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun                 4      0.19  0.0483    1.70 0.046  0.637  
Days                   1      0.03  0.0255    0.90 0.006  0.647  
T1D_Time_Interaction   1      0.25  0.2509    8.85 0.060  0.059 .
Age                    1      0.06  0.0580    2.05 0.014  0.620  
Parity                 1      0.08  0.0802    2.83 0.019  0.499  
BMI                    1      0.07  0.0675    2.38 0.016  0.692  
HLA                    2      0.05  0.0253    0.89 0.012  0.696  
T1Dstatus              1      0.02  0.0209    0.74 0.005  0.629  
Residuals            121      3.43  0.0284         0.821  0.689  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.059

11.1.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
SeqRun          3     0.093  0.0309    1.05 0.116  0.401   
Nulliparous     1     0.194  0.1940    6.58 0.242  0.007 **
Age_LMP         1     0.016  0.0158    0.54 0.020  0.576   
BMI_conception  1     0.008  0.0082    0.28 0.010  0.799   
HLA.6DRML       2     0.041  0.0207    0.70 0.052  0.593   
T1Dstatus       1     0.066  0.0658    2.23 0.082  0.109   
Residuals      13     0.383  0.0295         0.478          
Total          22     0.801                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.109

Beta diversity Plot

11.1.3 T1D status in trimester 2


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
seqRun     3     0.272  0.0907   2.694 0.171   0.68
Age        1     0.028  0.0285   0.846 0.018   0.63
Parity     1     0.025  0.0246   0.732 0.016   0.29
BMI        1     0.036  0.0356   1.058 0.022   0.44
HLA        2     0.030  0.0148   0.441 0.019   0.80
T1Dstatus  1     0.088  0.0877   2.604 0.055   0.11
Residuals 33     1.111  0.0337         0.699   0.40
Total     42     1.589                 1.000       

Beta diversity Plot

11.1.4 T1D status in trimester 3


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun     4     0.081  0.0202    0.87 0.046  0.485  
Age        1     0.016  0.0160    0.69 0.009  0.374  
Parity     1     0.116  0.1161    4.97 0.066  0.871  
BMI        1     0.114  0.1144    4.90 0.065  0.387  
HLA        2     0.028  0.0139    0.59 0.016  0.629  
T1Dstatus  1     0.062  0.0617    2.64 0.035  0.086 .
Residuals 57     1.331  0.0233         0.761  0.320  
Total     67     1.747                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

11.1.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.056  0.0282    1.86 0.042  0.437  
seqRun     3     0.175  0.0584    3.86 0.131  0.710  
Age        1     0.008  0.0077    0.51 0.006  0.924  
Parity     1     0.107  0.1065    7.04 0.080  0.139  
BMI        1     0.066  0.0656    4.33 0.049  0.455  
Days       1     0.047  0.0467    3.08 0.035  0.075 .
Residuals 58     0.878  0.0151         0.657  0.208  
Total     67     1.336                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

11.1.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.056  0.0282    1.87 0.042   0.44
seqRun     3     0.175  0.0584    3.86 0.131   0.71
Age        1     0.008  0.0077    0.51 0.006   0.93
Parity     1     0.107  0.1065    7.05 0.080   0.14
BMI        1     0.066  0.0656    4.34 0.049   0.43
Tri        2     0.063  0.0315    2.08 0.047   0.17
Residuals 57     0.862  0.0151         0.645   0.28
Total     67     1.336                 1.000       

Beta diversity Plot

11.1.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.191  0.0953    2.53 0.073  0.282  
seqRun     4     0.106  0.0266    0.71 0.041  0.869  
Age        1     0.188  0.1878    4.99 0.072  0.018 *
Parity     1     0.027  0.0267    0.71 0.010  0.873  
BMI        1     0.007  0.0072    0.19 0.003  0.743  
Days       1     0.013  0.0128    0.34 0.005  0.730  
Residuals 55     2.071  0.0377         0.796  0.323  
Total     65     2.603                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

11.1.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.191  0.0953    2.54 0.073  0.300  
seqRun     4     0.106  0.0266    0.71 0.041  0.845  
Age        1     0.188  0.1878    5.01 0.072  0.018 *
Parity     1     0.027  0.0267    0.71 0.010  0.874  
BMI        1     0.007  0.0072    0.19 0.003  0.738  
Tri        2     0.059  0.0297    0.79 0.023  0.843  
Residuals 54     2.025  0.0375         0.778  0.446  
Total     65     2.603                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

11.1.9 Other factors

11.1.9.1 Age at conception

11.1.9.1.1 Age at conception interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.49 0.020  0.568  
T1Dstatus              1      0.20  0.2033    7.18 0.049  0.052 .
seqRun                 4      0.22  0.0557    1.97 0.053  0.168  
Tri                    2      0.06  0.0308    1.09 0.015  0.816  
Age                    1      0.07  0.0666    2.35 0.016  0.450  
Parity                 1      0.07  0.0698    2.46 0.017  0.836  
BMI                    1      0.05  0.0530    1.87 0.013  0.954  
Age_Time_Interaction   1      0.02  0.0185    0.65 0.004  0.403  
Residuals            120      3.40  0.0283         0.813  0.427  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.1.2 Age at conception interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.49 0.020  0.546  
T1Dstatus              1      0.20  0.2033    7.16 0.049  0.063 .
seqRun                 4      0.22  0.0557    1.96 0.053  0.167  
Tri                    2      0.06  0.0308    1.08 0.015  0.810  
Age                    1      0.07  0.0666    2.34 0.016  0.480  
Parity                 1      0.07  0.0698    2.46 0.017  0.839  
BMI                    1      0.05  0.0530    1.87 0.013  0.955  
Age_Time_Interaction   1      0.01  0.0061    0.21 0.001  0.773  
Residuals            120      3.41  0.0284         0.816  0.446  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.1.3 Age at conception interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.50 0.020  0.542  
T1Dstatus              1      0.20  0.2033    7.20 0.049  0.054 .
seqRun                 4      0.22  0.0557    1.97 0.053  0.182  
Tri                    2      0.06  0.0308    1.09 0.015  0.820  
Age                    1      0.07  0.0666    2.36 0.016  0.445  
Parity                 1      0.07  0.0698    2.47 0.017  0.851  
BMI                    1      0.05  0.0530    1.88 0.013  0.956  
Age_Time_Interaction   1      0.03  0.0292    1.03 0.007  0.126  
Residuals            120      3.39  0.0282         0.811  0.363  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.1.4 Age at conception (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      0.08  0.0423    1.50 0.020  0.526  
T1Dstatus   1      0.20  0.2033    7.20 0.049  0.042 *
seqRun      4      0.22  0.0557    1.97 0.053  0.182  
Tri         2      0.06  0.0308    1.09 0.015  0.809  
Parity      1      0.07  0.0702    2.49 0.017  0.867  
BMI         1      0.05  0.0490    1.74 0.012  0.951  
Age         1      0.07  0.0702    2.49 0.017  0.498  
Residuals 121      3.42  0.0282         0.818  0.382  
Total     133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

11.1.9.2 Body max index (BMI)

11.1.9.2.1 BMI interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.49 0.020  0.556  
T1Dstatus              1      0.20  0.2033    7.17 0.049  0.045 *
seqRun                 4      0.22  0.0557    1.97 0.053  0.185  
Tri                    2      0.06  0.0308    1.09 0.015  0.813  
Age                    1      0.07  0.0666    2.35 0.016  0.490  
Parity                 1      0.07  0.0698    2.46 0.017  0.838  
BMI                    1      0.05  0.0530    1.87 0.013  0.956  
BMI_Time_Interaction   1      0.01  0.0136    0.48 0.003  0.582  
Residuals            120      3.40  0.0284         0.814  0.444  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.2.2 BMI interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.49 0.020  0.562  
T1Dstatus              1      0.20  0.2033    7.14 0.049  0.037 *
seqRun                 4      0.22  0.0557    1.96 0.053  0.180  
Tri                    2      0.06  0.0308    1.08 0.015  0.791  
Age                    1      0.07  0.0666    2.34 0.016  0.450  
Parity                 1      0.07  0.0698    2.45 0.017  0.840  
BMI                    1      0.05  0.0530    1.86 0.013  0.952  
BMI_Time_Interaction   1      0.00 -0.0010   -0.03 0.000  0.925  
Residuals            120      3.42  0.0285         0.818  0.415  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.2.3 BMI interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.49 0.020  0.546  
T1Dstatus              1      0.20  0.2033    7.16 0.049  0.042 *
seqRun                 4      0.22  0.0557    1.96 0.053  0.186  
Tri                    2      0.06  0.0308    1.08 0.015  0.804  
Age                    1      0.07  0.0666    2.35 0.016  0.468  
Parity                 1      0.07  0.0698    2.46 0.017  0.834  
BMI                    1      0.05  0.0530    1.87 0.013  0.944  
BMI_Time_Interaction   1      0.01  0.0072    0.25 0.002  0.668  
Residuals            120      3.41  0.0284         0.816  0.407  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.2.4 BMI (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA         2      0.08  0.0423    1.50 0.020  0.554  
T1Dstatus   1      0.20  0.2033    7.20 0.049  0.047 *
seqRun      4      0.22  0.0557    1.97 0.053  0.169  
Tri         2      0.06  0.0308    1.09 0.015  0.818  
Age         1      0.07  0.0666    2.36 0.016  0.477  
Parity      1      0.07  0.0698    2.47 0.017  0.848  
BMI         1      0.05  0.0530    1.88 0.013  0.962  
Residuals 121      3.42  0.0282         0.818  0.416  
Total     133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

11.1.9.3 HLA type

11.1.9.3.1 HLA type interaction with time (reference: DR34 )

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.49 0.020  0.579  
T1Dstatus              1      0.20  0.2033    7.14 0.049  0.042 *
Days                   1      0.01  0.0054    0.19 0.001  0.944  
seqRun                 4      0.24  0.0595    2.09 0.057  0.246  
Age                    1      0.06  0.0643    2.26 0.015  0.418  
Parity                 1      0.07  0.0724    2.54 0.017  0.826  
BMI                    1      0.05  0.0501    1.76 0.012  0.952  
HLA_Time_Interaction   1      0.01  0.0141    0.49 0.003  0.608  
Residuals            121      3.45  0.0285         0.825  0.329  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.3.2 HLA type interaction with time (reference: DRXX)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.49 0.020  0.565  
T1Dstatus              1      0.20  0.2033    7.14 0.049  0.051 .
Days                   1      0.01  0.0054    0.19 0.001  0.951  
seqRun                 4      0.24  0.0595    2.09 0.057  0.247  
Age                    1      0.06  0.0643    2.26 0.015  0.417  
Parity                 1      0.07  0.0724    2.54 0.017  0.813  
BMI                    1      0.05  0.0501    1.76 0.012  0.947  
HLA_Time_Interaction   1      0.02  0.0157    0.55 0.004  0.991  
Residuals            121      3.44  0.0285         0.824  0.555  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.3.3 HLA type interaction with time (reference: Group3o4)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.48 0.020  0.552  
T1Dstatus              1      0.20  0.2033    7.11 0.049  0.054 .
Days                   1      0.01  0.0054    0.19 0.001  0.938  
seqRun                 4      0.24  0.0595    2.08 0.057  0.234  
Age                    1      0.06  0.0643    2.25 0.015  0.409  
Parity                 1      0.07  0.0724    2.53 0.017  0.825  
BMI                    1      0.05  0.0501    1.75 0.012  0.952  
HLA_Time_Interaction   1      0.00  0.0006    0.02 0.000  0.932  
Residuals            121      3.46  0.0286         0.828  0.322  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.3.4 HLA type (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days        1      0.01  0.0098    0.35 0.002  0.854  
seqRun      4      0.21  0.0523    1.84 0.050  0.638  
Age         1      0.06  0.0606    2.14 0.014  0.603  
Parity      1      0.09  0.0940    3.32 0.023  0.316  
BMI         1      0.11  0.1051    3.70 0.025  0.325  
T1Dstatus   1      0.19  0.1889    6.66 0.045  0.046 *
HLA         2      0.05  0.0254    0.90 0.012  0.754  
Residuals 122      3.46  0.0284         0.828  0.272  
Total     133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

11.1.9.4 Parity

11.1.9.4.1 Parity interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                         Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                       2      0.08  0.0423    1.53 0.020  0.533  
T1Dstatus                 1      0.20  0.2033    7.36 0.049  0.050 *
Days                      1      0.01  0.0054    0.20 0.001  0.938  
seqRun                    4      0.24  0.0595    2.15 0.057  0.248  
Age                       1      0.06  0.0643    2.33 0.015  0.458  
Parity                    1      0.07  0.0724    2.62 0.017  0.814  
BMI                       1      0.05  0.0501    1.82 0.012  0.950  
Parity_Time_Interaction   1      0.12  0.1190    4.31 0.028  0.043 *
Residuals               121      3.34  0.0276         0.800  0.137  
Total                   133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.4.2 Parity (no interaction but within T1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.044  0.0222    0.65 0.055  0.638  
T1Dstatus  1     0.010  0.0097    0.28 0.012  0.839  
seqRun     1     0.067  0.0673    1.97 0.084  0.041 *
Age        1     0.029  0.0286    0.84 0.036  0.689  
BMI        1     0.018  0.0179    0.52 0.022  0.778  
Parity     1     0.122  0.1216    3.56 0.152  0.411  
Residuals 15     0.512  0.0341         0.639  0.750  
Total     22     0.801                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.4.3 Parity (no interaction but within T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.039  0.0193    0.53 0.024   0.77  
T1Dstatus  1     0.160  0.1599    4.42 0.101   0.05 *
seqRun     1     0.065  0.0652    1.80 0.041   0.92  
Age        1     0.032  0.0324    0.90 0.020   0.23  
BMI        1     0.012  0.0123    0.34 0.008   0.56  
Parity     1     0.015  0.0153    0.42 0.010   0.92  
Residuals 35     1.265  0.0362         0.796   0.53  
Total     42     1.589                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.4.4 Parity (no interaction but within T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.038  0.0192    0.80 0.022  0.561  
T1Dstatus  1     0.091  0.0912    3.81 0.052  0.058 .
seqRun     1     0.003  0.0029    0.12 0.002  0.076 .
Age        1     0.014  0.0143    0.60 0.008  0.663  
BMI        1     0.028  0.0280    1.17 0.016  0.875  
Parity     1     0.137  0.1373    5.74 0.079  0.836  
Residuals 60     1.435  0.0239         0.821  0.341  
Total     67     1.747                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

11.1.9.5 Mode of delivery

11.1.9.5.1 Mode of delivery interaction with time (reference: Emergency caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.48 0.020  0.549  
T1Dstatus              1      0.20  0.2033    7.13 0.049  0.045 *
MOD                    2      0.07  0.0366    1.28 0.018  0.615  
Days                   1      0.01  0.0052    0.18 0.001  0.942  
seqRun                 4      0.21  0.0520    1.82 0.050  0.418  
Age                    1      0.08  0.0821    2.88 0.020  0.220  
Parity                 1      0.07  0.0719    2.52 0.017  0.755  
BMI                    1      0.04  0.0382    1.34 0.009  0.956  
MOD_Time_Interaction   1      0.02  0.0156    0.55 0.004  0.991  
Residuals            119      3.40  0.0285         0.813  0.678  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.5.2 Mode of delivery interaction with time (reference: Elective caesarea)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.49 0.020  0.537  
T1Dstatus              1      0.20  0.2033    7.17 0.049  0.057 .
MOD                    2      0.07  0.0366    1.29 0.018  0.573  
Days                   1      0.01  0.0052    0.18 0.001  0.931  
seqRun                 4      0.21  0.0520    1.83 0.050  0.433  
Age                    1      0.08  0.0821    2.90 0.020  0.209  
Parity                 1      0.07  0.0719    2.54 0.017  0.736  
BMI                    1      0.04  0.0382    1.35 0.009  0.958  
MOD_Time_Interaction   1      0.04  0.0388    1.37 0.009  0.021 *
Residuals            119      3.37  0.0283         0.807  0.391  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.5.3 Mode of delivery interaction with time (reference: Labour)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                    2      0.08  0.0423    1.49 0.020  0.573  
T1Dstatus              1      0.20  0.2033    7.15 0.049  0.048 *
MOD                    2      0.07  0.0366    1.29 0.018  0.615  
Days                   1      0.01  0.0052    0.18 0.001  0.935  
seqRun                 4      0.21  0.0520    1.83 0.050  0.410  
Age                    1      0.08  0.0821    2.89 0.020  0.219  
Parity                 1      0.07  0.0719    2.53 0.017  0.724  
BMI                    1      0.04  0.0382    1.34 0.009  0.956  
MOD_Time_Interaction   1      0.03  0.0258    0.91 0.006  0.961  
Residuals            119      3.39  0.0285         0.810  0.652  
Total                133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.5.4 Mode of delivery (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days        1      0.01  0.0098    0.34 0.002  0.854  
seqRun      4      0.21  0.0523    1.84 0.050  0.629  
Age         1      0.06  0.0606    2.13 0.014  0.607  
Parity      1      0.09  0.0940    3.31 0.023  0.340  
BMI         1      0.11  0.1051    3.70 0.025  0.324  
HLA         2      0.09  0.0426    1.50 0.020  0.508  
T1Dstatus   1      0.15  0.1545    5.44 0.037  0.067 .
MOD         2      0.05  0.0242    0.85 0.012  0.740  
Residuals 120      3.41  0.0284         0.817  0.468  
Total     133      4.18                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.5.5 Mode of delivery (no interaction: T1)

Call:
adonis(formula = D ~ SeqRun + Nulliparous + BMI_conception +      T1Dstatus + Age_LMP + HLA.6DRML + MOD, data = Meta_df) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
SeqRun          3     0.093  0.0309    1.06 0.116  0.398   
Nulliparous     1     0.194  0.1940    6.67 0.242  0.009 **
BMI_conception  1     0.010  0.0103    0.35 0.013  0.749   
T1Dstatus       1     0.089  0.0887    3.05 0.111  0.060 . 
Age_LMP         1     0.013  0.0132    0.45 0.016  0.647   
HLA.6DRML       2     0.019  0.0096    0.33 0.024  0.879   
MOD             2     0.063  0.0316    1.09 0.079  0.373   
Residuals      11     0.320  0.0291         0.400          
Total          22     0.801                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.5.6 Mode of delivery (no interaction: T2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
Days       1     0.054  0.0544   1.573 0.034  0.736  
seqRun     3     0.247  0.0824   2.384 0.156  0.204  
Age        1     0.031  0.0307   0.887 0.019  0.657  
Parity     1     0.023  0.0232   0.670 0.015  0.199  
BMI        1     0.060  0.0605   1.749 0.038  0.789  
HLA        2     0.010  0.0051   0.147 0.006  0.966  
T1Dstatus  1     0.106  0.1063   3.075 0.067  0.065 .
MOD        2     0.020  0.0098   0.283 0.012  0.876  
Residuals 30     1.037  0.0346         0.653  0.751  
Total     42     1.589                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.5.7 Mode of delivery (no interaction: T3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
Days       1     0.091  0.0915    3.91 0.052   0.12
seqRun     4     0.071  0.0177    0.75 0.040   0.65
Age        1     0.012  0.0125    0.53 0.007   0.62
Parity     1     0.130  0.1304    5.57 0.075   0.37
BMI        1     0.106  0.1057    4.51 0.060   0.50
HLA        2     0.018  0.0089    0.38 0.010   0.77
T1Dstatus  1     0.027  0.0267    1.14 0.015   0.28
MOD        2     0.028  0.0140    0.60 0.016   0.61
Residuals 54     1.264  0.0234         0.724   0.64
Total     67     1.747                 1.000       

11.1.9.6 Carbohydrate intake

11.1.9.6.1 Carbohydrate interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.08  0.0404    1.42 0.019   0.58  
T1Dstatus               1      0.19  0.1887    6.65 0.045   0.06 .
Carbs                   1      0.02  0.0175    0.62 0.004   0.73  
seqRun                  4      0.25  0.0615    2.17 0.059   0.16  
Tri                     2      0.06  0.0317    1.12 0.015   0.73  
Age                     1      0.10  0.0967    3.41 0.023   0.14  
Parity                  1      0.06  0.0602    2.12 0.015   0.83  
BMI                     1      0.05  0.0524    1.85 0.013   0.88  
Carb_Time_Interaction   1      0.02  0.0243    0.85 0.006   0.75  
Residuals             117      3.32  0.0284         0.800   0.53  
Total                 131      4.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.6.2 Carbohydrate interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.08  0.0404    1.42 0.019  0.586  
T1Dstatus               1      0.19  0.1887    6.64 0.045  0.056 .
Carbs                   1      0.02  0.0175    0.62 0.004  0.738  
seqRun                  4      0.25  0.0615    2.16 0.059  0.168  
Tri                     2      0.06  0.0317    1.11 0.015  0.734  
Age                     1      0.10  0.0967    3.40 0.023  0.149  
Parity                  1      0.06  0.0602    2.12 0.015  0.794  
BMI                     1      0.05  0.0524    1.84 0.013  0.854  
Carb_Time_Interaction   1      0.02  0.0155    0.55 0.004  0.772  
Residuals             117      3.33  0.0284         0.802  0.490  
Total                 131      4.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.6.3 Carbohydrate interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                       Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                     2      0.08  0.0404    1.42 0.019  0.585  
T1Dstatus               1      0.19  0.1887    6.63 0.045  0.067 .
Carbs                   1      0.02  0.0175    0.62 0.004  0.720  
seqRun                  4      0.25  0.0615    2.16 0.059  0.175  
Tri                     2      0.06  0.0317    1.11 0.015  0.743  
Age                     1      0.10  0.0967    3.40 0.023  0.131  
Parity                  1      0.06  0.0602    2.11 0.015  0.808  
BMI                     1      0.05  0.0524    1.84 0.013  0.864  
Carb_Time_Interaction   1      0.01  0.0120    0.42 0.003  0.793  
Residuals             117      3.33  0.0285         0.803  0.476  
Total                 131      4.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.6.4 Carbohydrate (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun      4      0.21  0.0529    1.87 0.051  0.508  
Tri         2      0.07  0.0354    1.25 0.017  0.736  
Age         1      0.07  0.0678    2.39 0.016  0.647  
Parity      1      0.08  0.0805    2.84 0.019  0.376  
BMI         1      0.09  0.0913    3.22 0.022  0.603  
HLA         2      0.08  0.0379    1.34 0.018  0.572  
T1Dstatus   1      0.14  0.1435    5.06 0.035  0.073 .
Carbs       1      0.06  0.0644    2.27 0.016  0.272  
Residuals 118      3.34  0.0283         0.806  0.390  
Total     131      4.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

11.1.9.7 Fibre intake

11.1.9.7.1 Fibre interaction with time (reference: trimester 1)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.08  0.0404    1.40 0.019  0.601  
T1Dstatus                1      0.19  0.1887    6.54 0.045  0.057 .
Fiber                    1      0.01  0.0062    0.21 0.001  0.937  
seqRun                   4      0.23  0.0575    1.99 0.055  0.244  
Tri                      2      0.06  0.0297    1.03 0.014  0.761  
Age                      1      0.08  0.0826    2.86 0.020  0.294  
Parity                   1      0.07  0.0651    2.26 0.016  0.708  
BMI                      1      0.05  0.0463    1.60 0.011  0.913  
Fiber_Time_Interaction   1      0.01  0.0142    0.49 0.003  0.514  
Residuals              117      3.38  0.0289         0.814  0.554  
Total                  131      4.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.7.2 Fibre interaction with time (reference: trimester 2)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.08  0.0404    1.39 0.019  0.580  
T1Dstatus                1      0.19  0.1887    6.52 0.045  0.061 .
Fiber                    1      0.01  0.0062    0.21 0.001  0.926  
seqRun                   4      0.23  0.0575    1.99 0.055  0.259  
Tri                      2      0.06  0.0297    1.02 0.014  0.759  
Age                      1      0.08  0.0826    2.85 0.020  0.298  
Parity                   1      0.07  0.0651    2.25 0.016  0.726  
BMI                      1      0.05  0.0463    1.60 0.011  0.917  
Fiber_Time_Interaction   1      0.00  0.0042    0.14 0.001  0.749  
Residuals              117      3.39  0.0289         0.816  0.592  
Total                  131      4.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.7.3 Fibre interaction with time (reference: trimester 3)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                        Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA                      2      0.08  0.0404    1.40 0.019  0.561  
T1Dstatus                1      0.19  0.1887    6.54 0.045  0.053 .
Fiber                    1      0.01  0.0062    0.21 0.001  0.914  
seqRun                   4      0.23  0.0575    1.99 0.055  0.264  
Tri                      2      0.06  0.0297    1.03 0.014  0.791  
Age                      1      0.08  0.0826    2.86 0.020  0.265  
Parity                   1      0.07  0.0651    2.26 0.016  0.717  
BMI                      1      0.05  0.0463    1.60 0.011  0.920  
Fiber_Time_Interaction   1      0.01  0.0116    0.40 0.003  0.531  
Residuals              117      3.38  0.0289         0.814  0.552  
Total                  131      4.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.7.4 Fibre (no interaction)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

           Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun      4      0.21  0.0529    1.84 0.051  0.495  
Tri         2      0.07  0.0354    1.23 0.017  0.748  
Age         1      0.07  0.0678    2.36 0.016  0.680  
Parity      1      0.08  0.0805    2.80 0.019  0.373  
BMI         1      0.09  0.0913    3.18 0.022  0.611  
HLA         2      0.08  0.0379    1.32 0.018  0.562  
T1Dstatus   1      0.14  0.1435    4.99 0.035  0.079 .
Fiber       1      0.02  0.0176    0.61 0.004  0.664  
Residuals 118      3.39  0.0287         0.817  0.525  
Total     131      4.15                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

11.1.9.8 1,5-AG (glucose control measurement)

11.1.9.8.1 1,5-AG interaction with time

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)   
HLA                    2      0.12  0.0583    2.09 0.033  0.452   
T1Dstatus              1      0.24  0.2400    8.61 0.067  0.036 * 
Days                   1      0.01  0.0086    0.31 0.002  0.894   
seqRun                 3      0.14  0.0468    1.68 0.039  0.600   
Age                    1      0.10  0.0994    3.57 0.028  0.115   
Parity                 1      0.04  0.0434    1.56 0.012  0.895   
BMI                    1      0.01  0.0132    0.48 0.004  0.984   
AG15                   1      0.09  0.0850    3.05 0.024  0.007 **
AG15_T1D_Interaction   1      0.04  0.0356    1.28 0.010  0.861   
Residuals            100      2.79  0.0279         0.781  0.170   
Total                112      3.57                 1.000          
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.8.2 1,5-AG within T1D women

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.018  0.0090    0.59 0.019  0.911  
Days       1     0.046  0.0457    3.00 0.049  0.055 .
seqRun     3     0.124  0.0414    2.72 0.133  0.352  
Age        1     0.014  0.0139    0.91 0.015  0.258  
Parity     1     0.066  0.0660    4.33 0.071  0.458  
BMI        1     0.027  0.0270    1.77 0.029  0.279  
AG15       1     0.041  0.0413    2.71 0.044  0.023 *
Residuals 39     0.594  0.0152         0.639  0.198  
Total     49     0.930                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
11.1.9.8.3 1,5-AG interaction with time (within non-T1D women)

Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.156  0.0779    2.18 0.066  0.394  
Days       1     0.011  0.0112    0.31 0.005  0.728  
seqRun     3     0.084  0.0282    0.79 0.036  0.905  
Age        1     0.145  0.1454    4.07 0.062  0.063 .
Parity     1     0.018  0.0177    0.50 0.007  0.957  
BMI        1     0.010  0.0100    0.28 0.004  0.647  
AG15       1     0.079  0.0788    2.21 0.033  0.840  
Residuals 52     1.859  0.0358         0.787  0.734  
Total     62     2.363                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

12 Functional analysis (Pathways)

In order to functionally annotate the metagenomic data, we used Kraken2 to filter out human genes more stringently before running HUMAnN2 again. For each sample, the HUMAnN2 output contained the following files:

  • XX_pathcoverage.tsv: This file details the abundance of each pathway in the community as a function of the abundances of the pathway's component reactions, with each reaction's abundance computed as the sum over abundances of genes catalyzing the reaction. Pathways with zero abundance are not included in the file. Pathway abundance is proportional to the number of complete "copies" of the pathway in the community (from the HUMAnN2 manual).

  • XX_genefamilies.tsv: This file details the abundance of each gene family in the community. Gene families are groups of evolutionarily-related protein-coding sequences that often perform similar functions. Gene family abundance at the community level is stratified to show the contributions from known and unknown species. Individual species' abundance contributions sum to the community total abundance (from the HUMAnN2 manual).

  1. The genefamilies.csv file can contain a very large number of features depending on the complexity of your underlying sample. In order to simplify the exploration of gene family abundance data, users can regroup gene families into other functional categories (from the HUMAnN2 manual). Therefore, we regrouped our resulting gene families into MetaCyc reactions and Kegg Orthology (KO) functional categories, which has to be done in a per sample manner. Example:
  • humann2_regroup_table --input NGU5366A1_genefamilies.tsv --groups uniref90_ko --output ./NGU5366A1_genefamilies_Regrouped_KO.tsv
  1. HUMAnN2 quantifies genes and pathways in units of RPKs (reads per kilobase). These account for gene length but not sample sequencing depth. Therefore, a user will renormalize their samples prior to downstream analysis to relative abundance or copies per million (CPM) units. Both of these represent "total sum scaling (TSS)"-style normalization: in the former case, each sample is constrained to sum to 1, whereas in the latter case (CPMs) samples are constrained to sum to 1 million. Units out of 1 million are often more convenient for tables with many, many features (such as genefamilies.tsv tables). CPM as used here does not refer to unnormalized COUNTS per million, but rather copies per million. CPMs as used here are a generic analog of the TPM (transcript per million) unit in RNA-seq. You may wish to use the abbreviation CoPM for added clarity. (from the HUMAnN2 manual). We normilized the counts for each sample file for their three functional tables (XX_genefamilies.tsv, XX_genefamilies_Regrouped_KO.tsv and XX_genefamilies_Regrouped_MetaCyc.tsv) to CoPM. Example:
  • humann2_renorm_table --input NGU5366A1_genefamilies_Regrouped_KO.tsv --output NGU5366A1_genefamilies_Regrouped_KO_CoPM.tsv --units cpm
  1. Each normalized file, contained one sample. Therefore, in order to obtain a table with the functional profiles for all the samples, we need to join them into one. Example:
  • humann2_join_tables --input KO --output Pregnancy_genefamilies_KO_Rel.tsv --file_name Complete_genefamilies_Regrouped_KO_Rel.tsv
  1. The functional profiles are stratified, which means that the sum of the species abundance of a given gene gives the abundance of the gene at the community level. The stratification shows the contributions from known and unknown species to a given function. If we are interested in knowing if there is a significant difference in the abundance of a specific function at the community level (i.e. irrespective of which species is contributing to it), the abundances need to be unstratified prior to the analysis. This is done as in the following exmaple:
  • humann2_split_stratified_table --input Complete_genefamilies_Regrouped_KO_Rel.tsv --output Split/

The folder split will contain stratified and unstratified abundances.

Note: Scripts used for regrouping, normalization, joinning tables and stratification are part of HUMAnN2.

The resulting files for pathways, metacyc reactions and Kegg orthology (KO) gene categories were imported into R to process with the Phyloseq (https://github.com/joey711/phyloseq) and other packages. The analysis performed in R is described in this document.

12.1 Bar plots taxonomy

12.2 Functional Alpha diversity (Days)


Call:
geeglm(formula = Observed ~ t1dfactor * days_c + age_c + nullip + 
    bmi_c + HLA + SeqRun, data = DivCal_R_df, id = motherid, 
    corstr = "exchangeable")

 Coefficients:
                     Estimate   Std.err   Wald Pr(>|W|)    
(Intercept)         270.37171   8.69441 967.04  < 2e-16 ***
t1dfactorT1D         21.79016   6.07686  12.86  0.00034 ***
days_c                0.03589   0.06653   0.29  0.58952    
age_c                 0.67547   0.79963   0.71  0.39826    
nullipYes           -16.71466   6.44698   6.72  0.00952 ** 
bmi_c                 0.23971   0.69683   0.12  0.73085    
HLADRXX              15.41744   9.07571   2.89  0.08936 .  
HLAGroup3o4          13.17415   8.22482   2.57  0.10921    
SeqRun2              -1.79192   9.20810   0.04  0.84570    
SeqRun3               3.39900   8.12048   0.18  0.67553    
SeqRun4              15.49328   8.29136   3.49  0.06168 .  
SeqRun6              -3.62746   8.39669   0.19  0.66573    
t1dfactorT1D:days_c  -0.00592   0.09783   0.00  0.95178    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Correlation structure = exchangeable 
Estimated Scale Parameters:

            Estimate Std.err
(Intercept)     1096     132
  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha   0.0827   0.199
Number of clusters:   121  Maximum cluster size: 3 

12.3 Functional Alpha diversity (Trimesters)


Call:
geeglm(formula = Observed ~ t1dfactor * Tri + age_c + nullip + 
    bmi_c + HLA + SeqRun, data = DivCal_R_df, id = motherid, 
    corstr = "exchangeable")

 Coefficients:
                   Estimate Std.err   Wald Pr(>|W|)    
(Intercept)         259.491  12.474 432.76   <2e-16 ***
t1dfactorT1D         30.426  16.236   3.51   0.0609 .  
TriT2                17.406  11.315   2.37   0.1240    
TriT3                 9.483  11.851   0.64   0.4236    
age_c                 0.806   0.786   1.05   0.3055    
nullipYes           -16.770   6.377   6.92   0.0085 ** 
bmi_c                 0.169   0.726   0.05   0.8159    
HLADRXX              15.914   9.109   3.05   0.0806 .  
HLAGroup3o4          14.645   8.301   3.11   0.0777 .  
SeqRun2               1.314   8.441   0.02   0.8763    
SeqRun3               2.710   7.970   0.12   0.7338    
SeqRun4              14.999   8.025   3.49   0.0616 .  
SeqRun6              -4.398   8.293   0.28   0.5959    
t1dfactorT1D:TriT2  -16.864  18.267   0.85   0.3559    
t1dfactorT1D:TriT3   -5.873  17.982   0.11   0.7439    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Correlation structure = exchangeable 
Estimated Scale Parameters:

            Estimate Std.err
(Intercept)     1082     131
  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha   0.0646   0.208
Number of clusters:   121  Maximum cluster size: 3 

12.4 Alpha diversity (T1D vs. non-T1D categorical time [Trimester])

12.5 Beta diversity analysis

12.5.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun                 4     0.077  0.0193    1.33 0.037  0.904  
Days                   1     0.015  0.0148    1.02 0.007  0.743  
T1D_Time_Interaction   1     0.041  0.0406    2.79 0.019  0.021 *
Age                    1     0.041  0.0406    2.79 0.019  0.530  
Parity                 1     0.036  0.0360    2.48 0.017  0.344  
BMI                    1     0.027  0.0268    1.85 0.013  0.997  
HLA                    2     0.074  0.0371    2.56 0.035  0.149  
T1Dstatus              1     0.028  0.0284    1.95 0.014  0.388  
Residuals            121     1.757  0.0145         0.838  0.254  
Total                133     2.096                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.021

12.5.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3     0.037  0.0124   0.742 0.096  0.808  
Nulliparous     1     0.029  0.0288   1.715 0.074  0.079 .
Age_LMP         1     0.021  0.0211   1.256 0.054  0.212  
BMI_conception  1     0.013  0.0130   0.775 0.033  0.627  
HLA.6DRML       2     0.039  0.0195   1.164 0.100  0.253  
T1Dstatus       1     0.033  0.0333   1.984 0.085  0.062 .
Residuals      13     0.218  0.0168         0.558         
Total          22     0.391                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.062

Beta diversity Plot

12.5.3 T1D status in trimester 2


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
seqRun     3     0.063  0.0211   1.518 0.101   0.57
Age        1     0.019  0.0194   1.399 0.031   0.60
Parity     1     0.014  0.0143   1.032 0.023   0.24
BMI        1     0.014  0.0138   0.989 0.022   0.95
HLA        2     0.033  0.0164   1.183 0.052   0.62
T1Dstatus  1     0.027  0.0273   1.962 0.043   0.10
Residuals 33     0.459  0.0139         0.728   0.30
Total     42     0.630                 1.000       

Beta diversity Plot

12.5.4 T1D status in trimester 3


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun     4     0.050  0.0124   0.809 0.047  0.502  
Age        1     0.016  0.0162   1.051 0.015  0.369  
Parity     1     0.028  0.0278   1.811 0.026  0.369  
BMI        1     0.023  0.0228   1.484 0.022  0.762  
HLA        2     0.036  0.0180   1.173 0.034  0.325  
T1Dstatus  1     0.025  0.0254   1.653 0.024  0.094 .
Residuals 57     0.877  0.0154         0.831  0.306  
Total     67     1.055                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

12.5.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.055  0.0275    2.05 0.050  0.495  
seqRun     3     0.092  0.0306    2.28 0.084  0.249  
Age        1     0.028  0.0279    2.08 0.025  0.921  
Parity     1     0.094  0.0944    7.04 0.086  0.083 .
BMI        1     0.038  0.0377    2.81 0.034  0.505  
Days       1     0.013  0.0127    0.95 0.012  0.234  
Residuals 58     0.777  0.0134         0.709  0.181  
Total     67     1.096                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

12.5.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.055  0.0275    2.03 0.050  0.483  
seqRun     3     0.092  0.0306    2.27 0.084  0.271  
Age        1     0.028  0.0279    2.07 0.025  0.900  
Parity     1     0.094  0.0944    6.99 0.086  0.072 .
BMI        1     0.038  0.0377    2.79 0.034  0.523  
Tri        2     0.021  0.0103    0.76 0.019  0.443  
Residuals 57     0.769  0.0135         0.702  0.211  
Total     67     1.096                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

12.5.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.063  0.0315   2.292 0.066  0.251  
seqRun     4     0.052  0.0130   0.946 0.055  0.998  
Age        1     0.043  0.0434   3.157 0.045  0.014 *
Parity     1     0.018  0.0176   1.279 0.018  0.944  
BMI        1     0.010  0.0102   0.740 0.011  0.871  
Days       1     0.012  0.0116   0.842 0.012  0.701  
Residuals 55     0.756  0.0138         0.793  0.613  
Total     65     0.954                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

12.5.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.063  0.0315   2.262 0.066  0.257  
seqRun     4     0.052  0.0130   0.934 0.055  1.000  
Age        1     0.043  0.0434   3.117 0.045  0.011 *
Parity     1     0.018  0.0176   1.263 0.018  0.945  
BMI        1     0.010  0.0102   0.731 0.011  0.869  
Tri        2     0.016  0.0079   0.565 0.016  0.955  
Residuals 54     0.752  0.0139         0.788  0.787  
Total     65     0.954                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

13 Functional analysis (Kegg Orthology)

13.1 Bar plots taxonomy

13.2 Functional Alpha diversity (Days)


Call:
geeglm(formula = Observed ~ t1dfactor * days_c + age_c + nullip + 
    bmi_c + HLA + SeqRun, data = DivCal_R_df, id = motherid, 
    corstr = "exchangeable")

 Coefficients:
                    Estimate  Std.err   Wald Pr(>|W|)    
(Intercept)         3200.574  121.672 691.94   <2e-16 ***
t1dfactorT1D         219.495   86.247   6.48   0.0109 *  
days_c                 0.274    0.848   0.10   0.7465    
age_c                  7.818   11.420   0.47   0.4936    
nullipYes           -261.839   90.461   8.38   0.0038 ** 
bmi_c                 -0.968    9.683   0.01   0.9203    
HLADRXX               69.320  123.799   0.31   0.5755    
HLAGroup3o4          115.169  115.933   0.99   0.3205    
SeqRun2              185.229  117.657   2.48   0.1154    
SeqRun3                9.051  111.436   0.01   0.9353    
SeqRun4              159.762  115.219   1.92   0.1656    
SeqRun6              -89.142  123.508   0.52   0.4704    
t1dfactorT1D:days_c   -0.199    1.331   0.02   0.8810    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Correlation structure = exchangeable 
Estimated Scale Parameters:

            Estimate Std.err
(Intercept)   209774   24094
  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha    0.149   0.203
Number of clusters:   121  Maximum cluster size: 3 

13.3 Functional Alpha diversity (Trimesters)


Call:
geeglm(formula = Observed ~ t1dfactor * Tri + age_c + nullip + 
    bmi_c + HLA + SeqRun, data = DivCal_R_df, id = motherid, 
    corstr = "exchangeable")

 Coefficients:
                   Estimate Std.err   Wald Pr(>|W|)    
(Intercept)         3109.43  174.67 316.90   <2e-16 ***
t1dfactorT1D         297.46  220.68   1.82   0.1777    
TriT2                170.29  156.08   1.19   0.2753    
TriT3                 65.86  156.99   0.18   0.6749    
age_c                  9.14   11.22   0.66   0.4154    
nullipYes           -263.11   89.64   8.62   0.0033 ** 
bmi_c                 -1.78   10.03   0.03   0.8593    
HLADRXX               72.70  124.59   0.34   0.5595    
HLAGroup3o4          129.58  116.47   1.24   0.2659    
SeqRun2              220.43  109.43   4.06   0.0440 *  
SeqRun3                1.41  110.02   0.00   0.9898    
SeqRun4              152.01  112.79   1.82   0.1778    
SeqRun6              -96.81  121.95   0.63   0.4273    
t1dfactorT1D:TriT2  -147.61  252.06   0.34   0.5581    
t1dfactorT1D:TriT3   -53.76  242.41   0.05   0.8245    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Correlation structure = exchangeable 
Estimated Scale Parameters:

            Estimate Std.err
(Intercept)   207892   24295
  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha    0.129   0.201
Number of clusters:   121  Maximum cluster size: 3 

13.4 Beta diversity analysis

13.4.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun                 4      0.19  0.0480    1.94 0.052  0.260  
Days                   1      0.05  0.0511    2.07 0.014  0.087 .
T1D_Time_Interaction   1      0.13  0.1288    5.22 0.035  0.034 *
Age                    1      0.09  0.0855    3.46 0.023  0.827  
Parity                 1      0.05  0.0493    1.99 0.013  0.073 .
BMI                    1      0.06  0.0603    2.44 0.016  0.994  
HLA                    2      0.10  0.0507    2.05 0.027  0.340  
T1Dstatus              1      0.04  0.0378    1.53 0.010  0.674  
Residuals            121      2.99  0.0247         0.809  0.217  
Total                133      3.69                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.034

13.4.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
SeqRun          3     0.070  0.0234   0.783 0.103  0.760  
Nulliparous     1     0.044  0.0440   1.474 0.065  0.139  
Age_LMP         1     0.034  0.0343   1.149 0.050  0.278  
BMI_conception  1     0.021  0.0207   0.693 0.030  0.756  
HLA.6DRML       2     0.056  0.0281   0.942 0.083  0.501  
T1Dstatus       1     0.066  0.0660   2.212 0.097  0.022 *
Residuals      13     0.388  0.0298         0.571         
Total          22     0.679                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.022

Beta diversity Plot

13.4.3 T1D status in trimester 2


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     3     0.130  0.0434    1.83 0.116  0.001 ***
Age        1     0.031  0.0314    1.32 0.028  0.509    
Parity     1     0.033  0.0334    1.41 0.030  0.001 ***
BMI        1     0.027  0.0275    1.16 0.025  0.505    
HLA        2     0.060  0.0299    1.26 0.053  0.467    
T1Dstatus  1     0.055  0.0548    2.31 0.049  0.062 .  
Residuals 33     0.782  0.0237         0.699  0.156    
Total     42     1.119                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

13.4.4 T1D status in trimester 3


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)    
seqRun     4     0.125  0.0311   1.216 0.068  0.502    
Age        1     0.041  0.0408   1.593 0.022  0.374    
Parity     1     0.031  0.0315   1.229 0.017  0.001 ***
BMI        1     0.062  0.0619   2.416 0.034  0.502    
HLA        2     0.045  0.0223   0.869 0.024  0.742    
T1Dstatus  1     0.055  0.0553   2.159 0.030  0.026 *  
Residuals 57     1.460  0.0256         0.803  0.181    
Total     67     1.818                 1.000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

13.4.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.095  0.0477    2.09 0.052  0.430  
seqRun     3     0.170  0.0565    2.48 0.093  0.287  
Age        1     0.042  0.0418    1.83 0.023  0.954  
Parity     1     0.086  0.0859    3.77 0.047  0.319  
BMI        1     0.080  0.0798    3.50 0.044  0.421  
Days       1     0.032  0.0321    1.41 0.018  0.087 .
Residuals 58     1.321  0.0228         0.724  0.339  
Total     67     1.825                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

13.4.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
HLA        2     0.095  0.0477    2.08 0.052   0.45
seqRun     3     0.170  0.0565    2.47 0.093   0.26
Age        1     0.042  0.0418    1.83 0.023   0.95
Parity     1     0.086  0.0859    3.75 0.047   0.30
BMI        1     0.080  0.0798    3.49 0.044   0.41
Tri        2     0.049  0.0246    1.08 0.027   0.12
Residuals 57     1.304  0.0229         0.714   0.33
Total     67     1.825                 1.000       

Beta diversity Plot

13.4.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.126  0.0629    2.65 0.073  0.186  
seqRun     4     0.127  0.0317    1.34 0.073  0.961  
Age        1     0.102  0.1024    4.32 0.059  0.014 *
Parity     1     0.020  0.0197    0.83 0.011  0.985  
BMI        1     0.019  0.0193    0.81 0.011  0.702  
Days       1     0.029  0.0289    1.22 0.017  0.438  
Residuals 55     1.303  0.0237         0.755  0.210  
Total     65     1.726                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

13.4.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.126  0.0629    2.63 0.073  0.218  
seqRun     4     0.127  0.0317    1.33 0.073  0.970  
Age        1     0.102  0.1024    4.29 0.059  0.011 *
Parity     1     0.020  0.0197    0.83 0.011  0.976  
BMI        1     0.019  0.0193    0.81 0.011  0.721  
Tri        2     0.043  0.0213    0.89 0.025  0.847  
Residuals 54     1.289  0.0239         0.747  0.372  
Total     65     1.726                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

14 Functional analysis (MetaCyc reactions)

14.1 Bar plots taxonomy

14.2 Functional Alpha diversity (Days)


Call:
geeglm(formula = Observed ~ t1dfactor * days_c + age_c + nullip + 
    bmi_c + HLA + SeqRun, data = DivCal_R_df, id = motherid, 
    corstr = "exchangeable")

 Coefficients:
                     Estimate   Std.err    Wald Pr(>|W|)    
(Intercept)         2004.5197   46.2156 1881.24  < 2e-16 ***
t1dfactorT1D         105.8145   32.0574   10.90  0.00096 ***
days_c                 0.1934    0.3213    0.36  0.54726    
age_c                  2.3352    4.0931    0.33  0.56832    
nullipYes            -83.7932   34.0845    6.04  0.01396 *  
bmi_c                 -0.0288    3.5634    0.00  0.99354    
HLADRXX               43.0525   45.9961    0.88  0.34927    
HLAGroup3o4           60.5172   42.0367    2.07  0.14997    
SeqRun2               28.8027   45.5925    0.40  0.52755    
SeqRun3               24.6452   41.1787    0.36  0.54951    
SeqRun4               75.2434   42.4728    3.14  0.07647 .  
SeqRun6              -34.6553   45.9168    0.57  0.45040    
t1dfactorT1D:days_c   -0.2802    0.5178    0.29  0.58846    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Correlation structure = exchangeable 
Estimated Scale Parameters:

            Estimate Std.err
(Intercept)    28904    4037
  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha   0.0329   0.222
Number of clusters:   121  Maximum cluster size: 3 

14.3 Functional Alpha diversity (Trimesters)


Call:
geeglm(formula = Observed ~ t1dfactor * Tri + age_c + nullip + 
    bmi_c + HLA + SeqRun, data = DivCal_R_df, id = motherid, 
    corstr = "exchangeable")

 Coefficients:
                   Estimate  Std.err   Wald Pr(>|W|)    
(Intercept)        1948.280   65.637 881.06   <2e-16 ***
t1dfactorT1D        168.710   87.379   3.73    0.054 .  
TriT2                92.654   59.743   2.41    0.121    
TriT3                50.426   59.210   0.73    0.394    
age_c                 2.992    3.993   0.56    0.454    
nullipYes           -84.967   33.584   6.40    0.011 *  
bmi_c                -0.517    3.730   0.02    0.890    
HLADRXX              43.247   46.673   0.86    0.354    
HLAGroup3o4          66.236   42.588   2.42    0.120    
SeqRun2              46.402   41.861   1.23    0.268    
SeqRun3              22.509   40.371   0.31    0.577    
SeqRun4              73.316   40.851   3.22    0.073 .  
SeqRun6             -38.003   45.246   0.71    0.401    
t1dfactorT1D:TriT2  -92.463   98.478   0.88    0.348    
t1dfactorT1D:TriT3  -61.983   95.940   0.42    0.518    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Correlation structure = exchangeable 
Estimated Scale Parameters:

            Estimate Std.err
(Intercept)    28520    4103
  Link = identity 

Estimated Correlation Parameters:
      Estimate Std.err
alpha 0.000515   0.221
Number of clusters:   121  Maximum cluster size: 3 

14.4 Beta diversity analysis

14.4.1 Interaction between T1D status and Time


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

                      Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
seqRun                 4     0.088  0.0221    1.55 0.044  0.748  
Days                   1     0.020  0.0200    1.40 0.010  0.295  
T1D_Time_Interaction   1     0.040  0.0405    2.84 0.020  0.065 .
Age                    1     0.040  0.0403    2.83 0.020  0.830  
Parity                 1     0.030  0.0300    2.10 0.015  0.463  
BMI                    1     0.027  0.0273    1.91 0.013  0.989  
HLA                    2     0.043  0.0213    1.49 0.021  0.660  
T1Dstatus              1     0.016  0.0157    1.10 0.008  0.804  
Residuals            121     1.727  0.0143         0.850  0.880  
Total                133     2.032                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
[1] 0.065

14.4.2 T1D status in trimester 1


Call:
adonis(formula = D ~ SeqRun + Nulliparous + Age_LMP + BMI_conception +      HLA.6DRML + T1Dstatus, data = Meta_dfTri) 

Permutation: free
Number of permutations: 999

Terms added sequentially (first to last)

               Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
SeqRun          3     0.030  0.0100   0.650 0.092   0.90
Nulliparous     1     0.022  0.0221   1.439 0.068   0.15
Age_LMP         1     0.010  0.0101   0.658 0.031   0.76
BMI_conception  1     0.021  0.0213   1.383 0.065   0.18
HLA.6DRML       2     0.022  0.0110   0.717 0.067   0.79
T1Dstatus       1     0.021  0.0212   1.377 0.065   0.21
Residuals      13     0.200  0.0154         0.612       
Total          22     0.327                 1.000       
[1] 0.207

Beta diversity Plot

14.4.3 T1D status in trimester 2


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
seqRun     3     0.080  0.0267   1.953 0.128   0.96
Age        1     0.021  0.0213   1.555 0.034   0.66
Parity     1     0.012  0.0123   0.895 0.020   0.51
BMI        1     0.012  0.0124   0.906 0.020   0.65
HLA        2     0.024  0.0118   0.861 0.038   0.82
T1Dstatus  1     0.023  0.0231   1.686 0.037   0.17
Residuals 33     0.452  0.0137         0.723   0.57
Total     42     0.625                 1.000       

Beta diversity Plot

14.4.4 T1D status in trimester 3


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)
seqRun     4     0.041  0.0102   0.637 0.038   0.51
Age        1     0.020  0.0204   1.278 0.019   0.36
Parity     1     0.029  0.0285   1.786 0.027   0.51
BMI        1     0.018  0.0181   1.137 0.017   0.73
HLA        2     0.023  0.0116   0.726 0.022   0.81
T1Dstatus  1     0.017  0.0171   1.069 0.016   0.35
Residuals 57     0.910  0.0160         0.860   0.87
Total     67     1.058                 1.000       

Beta diversity Plot

14.4.5 Days within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.034  0.0172    1.49 0.037  0.807  
seqRun     3     0.087  0.0289    2.49 0.094  0.309  
Age        1     0.024  0.0238    2.05 0.026  0.611  
Parity     1     0.060  0.0603    5.20 0.065  0.055 .
BMI        1     0.040  0.0401    3.46 0.043  0.499  
Days       1     0.009  0.0089    0.76 0.010  0.438  
Residuals 58     0.672  0.0116         0.726  0.414  
Total     67     0.926                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

14.4.6 Trimester within T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.034  0.0172    1.47 0.037  0.790  
seqRun     3     0.087  0.0289    2.47 0.094  0.287  
Age        1     0.024  0.0238    2.03 0.026  0.635  
Parity     1     0.060  0.0603    5.15 0.065  0.076 .
BMI        1     0.040  0.0401    3.42 0.043  0.527  
Tri        2     0.014  0.0070    0.60 0.015  0.678  
Residuals 57     0.667  0.0117         0.720  0.466  
Total     67     0.926                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

14.4.7 Days within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.070  0.0348   2.256 0.066  0.284  
seqRun     4     0.050  0.0125   0.813 0.047  0.999  
Age        1     0.045  0.0455   2.948 0.043  0.018 *
Parity     1     0.017  0.0173   1.122 0.016  0.919  
BMI        1     0.015  0.0149   0.965 0.014  0.128  
Days       1     0.012  0.0124   0.803 0.012  0.515  
Residuals 55     0.848  0.0154         0.802  0.619  
Total     65     1.058                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot

14.4.8 Trimester within non-T1D


Call:
adonis(formula = D ~ ., data = mtdat[, metadata_order, drop = F],      permutations = 0) 

Permutation: free
Number of permutations: 0

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model    R2 Pr(>F)  
HLA        2     0.070  0.0348   2.225 0.066   0.27  
seqRun     4     0.050  0.0125   0.802 0.047   1.00  
Age        1     0.045  0.0455   2.906 0.043   0.02 *
Parity     1     0.017  0.0173   1.106 0.016   0.93  
BMI        1     0.015  0.0149   0.952 0.014   0.13  
Tri        2     0.016  0.0080   0.511 0.015   0.93  
Residuals 54     0.845  0.0156         0.798   0.75  
Total     65     1.058                 1.000         
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Beta diversity Plot